Contacts of the helix formed by residues 1074 - 1103 (chain D) in PDB entry 6AH0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY1074 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP 6.2 0.4 - - - -
1072D LEU* 3.6 9.1 - - - +
1073D GLU* 1.3 78.0 - - - +
1075D PHE* 1.3 62.7 + - - -
1076D ALA 3.5 2.7 - - - -
1077D LEU* 3.8 6.1 + - - -
1078D MET* 3.4 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1075 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP* 5.2 11.9 - - - +
1073D GLU 3.6 2.4 + - - -
1074D GLY* 1.3 69.9 - - - -
1076D ALA* 1.3 66.6 + - - +
1077D LEU 3.2 0.2 - - - -
1078D MET* 2.9 12.1 + - - +
1079D ALA* 3.0 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1076 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP* 5.2 8.4 - - - +
1074D GLY* 3.5 0.6 - - - -
1075D PHE* 1.3 77.0 - - - +
1077D LEU* 1.3 55.9 + - - +
1079D ALA* 3.5 1.0 + - - -
1080D ASP* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1077 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074D GLY* 3.8 8.1 + - - -
1075D PHE 3.2 0.4 - - - -
1076D ALA* 1.3 72.6 - - - +
1078D MET* 1.3 61.0 + - - +
1080D ASP* 4.5 1.3 - - - +
1081D MET* 2.8 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1078 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072D LEU* 5.8 4.6 - - - +
1074D GLY 3.4 11.4 + - - -
1075D PHE* 2.9 8.6 + - - +
1077D LEU* 1.3 74.8 - - - +
1079D ALA* 1.3 63.2 + - - +
1081D MET* 3.0 4.4 + - - +
1082D VAL* 2.9 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1079 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836D PRO* 5.4 6.1 - - - +
1075D PHE 3.0 11.6 + - - -
1076D ALA* 3.9 2.2 - - - +
1078D MET* 1.3 72.5 - - - +
1080D ASP* 1.3 63.8 + - - +
1082D VAL* 3.3 3.7 + - - +
1083D TYR* 3.0 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1080 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836D PRO* 5.2 12.2 - - - +
1076D ALA 2.9 16.2 + - - -
1077D LEU* 3.7 3.8 - - - +
1079D ALA* 1.3 74.4 - - - +
1081D MET* 1.3 61.6 + - - +
1083D TYR* 3.0 4.9 + - - +
1084D VAL* 2.9 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1081 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062D LEU* 5.5 15.6 - - - +
1077D LEU 2.8 18.5 + - - -
1078D MET* 3.5 3.1 - - - +
1080D ASP* 1.3 70.7 - - - +
1082D VAL* 1.3 63.8 + - - +
1084D VAL* 3.1 2.7 + - - +
1085D THR* 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1082 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078D MET 2.9 13.2 + - - -
1079D ALA* 3.6 4.0 - - - +
1080D ASP 3.2 0.2 - - - -
1081D MET* 1.3 75.4 - - - +
1083D TYR* 1.3 61.5 + - - +
1085D THR* 3.3 1.0 + - - +
1086D GLN* 2.9 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1083 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836D PRO* 6.3 3.6 - - - -
1079D ALA 3.0 9.9 + - - -
1080D ASP* 3.0 8.2 + - - +
1082D VAL* 1.3 74.8 - - - +
1084D VAL* 1.3 63.1 + - - +
1086D GLN* 3.9 0.8 - - - +
1087D SER* 3.0 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1084 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063D LEU* 6.4 1.6 - - - -
1080D ASP 2.9 12.7 + - - -
1081D MET* 3.6 3.6 - - - +
1083D TYR* 1.3 76.5 - - - +
1085D THR* 1.3 56.4 + - - +
1087D SER* 3.5 1.0 + - - -
1088D ALA* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1085 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063D LEU* 6.1 5.7 - - - +
1081D MET 2.9 14.8 + - - -
1082D VAL* 3.8 0.7 - - - +
1084D VAL* 1.3 72.8 - - - +
1086D GLN* 1.3 65.9 + - - +
1088D ALA* 3.2 12.9 + - - +
1089D GLY 3.7 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1086 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082D VAL 2.9 15.8 + - - -
1083D TYR 3.9 0.9 - - - -
1085D THR* 1.3 78.5 - - - +
1087D SER* 1.3 61.2 + - - +
1088D ALA 3.3 0.3 + - - -
1089D GLY* 3.6 7.4 + - - -
1090D ARG 4.7 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1087 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083D TYR 3.0 15.9 + - - -
1084D VAL 3.8 1.6 - - - -
1086D GLN* 1.3 75.8 - - - +
1088D ALA* 1.3 61.5 + - - +
1089D GLY 3.2 0.9 + - - -
1090D ARG* 3.4 4.2 + - - -
1091D LEU* 3.0 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1088 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084D VAL 2.9 17.0 + - - -
1085D THR* 3.2 6.5 + - - +
1086D GLN 3.1 1.4 - - - -
1087D SER* 1.3 75.1 - - - +
1089D GLY* 1.3 60.3 + - - +
1091D LEU* 4.4 2.0 - - - +
1092D MET* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1089 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085D THR 3.7 4.6 + - - -
1086D GLN 3.6 7.4 + - - -
1087D SER 3.2 1.6 + - - -
1088D ALA* 1.3 76.8 - - - +
1090D ARG* 1.3 62.2 + - - +
1092D MET 4.0 0.2 - - - -
1093D ARG* 3.0 22.2 + - - -
1115D CYS* 6.1 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1090 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991D TYR* 4.6 23.2 - - - +
1086D GLN 4.7 2.0 + - - -
1087D SER 3.4 5.6 + - - -
1089D GLY* 1.3 73.7 - - - +
1091D LEU* 1.3 63.3 + - - +
1093D ARG* 3.3 1.8 + - - +
1094D ALA* 2.9 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1091 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087D SER 3.0 14.9 + - - -
1088D ALA* 3.9 2.7 - - - +
1090D ARG* 1.3 74.4 - - - +
1092D MET* 1.3 62.7 + - - +
1094D ALA* 3.1 4.0 + - - +
1095D ILE* 3.0 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1092 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088D ALA 2.9 19.3 + - - -
1089D GLY 4.1 0.2 - - - -
1091D LEU* 1.3 72.5 - - - +
1093D ARG* 1.3 56.6 + - - +
1095D ILE* 3.2 4.5 + - - +
1096D PHE* 2.9 24.3 + - - -
1111D THR* 4.8 11.1 - - - +
1115D CYS* 5.9 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1093 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089D GLY 3.0 17.4 + - - -
1090D ARG* 3.7 1.6 - - - +
1092D MET* 1.3 75.1 - - - +
1094D ALA* 1.3 57.9 + - - +
1096D PHE* 3.2 2.7 + - - +
1097D GLU* 2.9 26.5 + - - -
1115D CYS* 5.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1094 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987D ILE* 5.3 13.4 - - - +
991D TYR* 6.1 2.9 - - - +
1090D ARG 2.9 14.6 + - - -
1091D LEU 3.1 2.9 + - - -
1093D ARG* 1.3 72.7 - - - +
1095D ILE* 1.3 65.4 + - - +
1097D GLU* 3.5 1.8 + - - +
1098D ILE* 3.0 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1095 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091D LEU 3.0 13.5 + - - -
1092D MET* 3.5 4.9 - - - +
1093D ARG 3.2 0.4 - - - -
1094D ALA* 1.3 76.2 - - - +
1096D PHE* 1.3 61.4 + - - +
1098D ILE* 3.2 1.1 + - - +
1099D VAL* 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1096 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092D MET 2.9 16.2 + - - -
1093D ARG* 3.2 4.2 + - - +
1095D ILE* 1.3 70.9 - - - +
1097D GLU* 1.3 64.5 + - - +
1099D VAL* 3.2 0.7 + - - +
1100D LEU* 2.9 23.2 + - - -
1108D THR* 5.3 9.4 - - - +
1111D THR* 5.2 16.9 - - - +
1112D LEU* 5.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1097 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093D ARG 2.9 15.3 + - - -
1094D ALA* 3.9 2.5 - - - +
1096D PHE* 1.3 73.6 - - - +
1098D ILE* 1.3 55.8 + - - +
1100D LEU* 3.9 1.0 - - - +
1101D ASN* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1098 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094D ALA 3.0 14.9 + - - -
1095D ILE* 3.7 2.9 - - - +
1097D GLU* 1.3 74.0 - - - +
1099D VAL* 1.3 56.4 + - - +
1101D ASN* 3.1 3.9 + - - +
1102D ARG* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1099 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095D ILE 2.9 14.5 + - - -
1096D PHE* 3.7 1.1 - - - +
1098D ILE* 1.3 75.1 - - - +
1100D LEU* 1.3 56.5 + - - +
1102D ARG* 3.7 3.0 + - - +
1103D GLY 3.3 4.3 + - - -
1104D TRP* 3.3 30.5 + - - +
1107D LEU 6.2 0.9 - - - -
1108D THR* 5.2 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096D PHE 2.9 15.4 + - - -
1097D GLU* 3.9 1.1 - - - +
1099D VAL* 1.3 75.5 - - - +
1101D ASN* 1.3 65.4 + - - +
1102D ARG 3.1 1.6 - - - -
1103D GLY* 3.0 15.4 + - - +
1104D TRP 5.1 0.7 - - - +
1108D THR* 5.2 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097D GLU 3.0 15.7 + - - -
1098D ILE 3.6 4.0 - - - -
1100D LEU* 1.3 76.0 - - - +
1102D ARG* 1.3 60.1 + - - +
1103D GLY* 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098D ILE 3.0 13.9 + - - -
1099D VAL* 3.7 4.0 + - - +
1100D LEU 3.1 0.2 - - - -
1101D ASN* 1.3 79.0 - - - +
1103D GLY* 1.3 58.1 + - - +
1104D TRP 3.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099D VAL 3.3 1.4 + - - -
1100D LEU* 3.0 17.6 + - - -
1101D ASN 4.5 0.2 - - - -
1102D ARG* 1.3 78.8 - - - +
1104D TRP* 1.3 59.1 + - - +
1105D ALA* 3.3 2.6 + - - -
1232D VAL* 3.8 3.8 - - - -
1233D ILE* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il