Contacts of the helix formed by residues 1079 - 1094 (chain A) in PDB entry 1OFD
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 PRO1079 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LEU* 4.2 21.5 - - + -
496A LYS* 6.2 0.2 - - - -
735A ILE* 3.5 19.3 - - + -
842A LEU* 4.0 26.0 - - + +
1037A ALA* 3.3 3.5 - - - +
1061A HIS* 3.5 20.8 - - + +
1077A GLY 4.9 0.2 - - - +
1078A SER* 1.3 93.3 - - - +
1080A TRP* 1.3 63.8 + - - +
1081A GLU* 3.5 18.2 - - - +
1082A LEU* 3.2 18.6 + - + +
1083A GLY 3.2 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1080 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A ARG* 3.1 48.9 - - - +
1037A ALA* 4.2 5.2 - - - -
1058A ILE* 4.6 3.4 - - + +
1059A SER 4.6 1.6 - - - -
1060A GLY* 3.8 21.1 - - - +
1061A HIS* 5.0 0.2 + - - -
1062A ASP* 5.0 2.5 - - + -
1078A SER 3.6 1.6 + - - -
1079A PRO* 1.3 69.6 - - - +
1081A GLU* 1.3 73.7 + - + +
1083A GLY* 2.9 2.2 + - - +
1084A VAL* 2.7 55.1 + - + +
1104A ALA* 4.8 3.8 - - + -
1105A ASP 3.7 18.2 - - - +
1106A GLY* 3.0 30.2 + - - -
1108A LEU* 3.7 20.6 - - + +
1113A ASP 4.2 1.8 - - - -
1116A MET* 4.2 3.1 - - + -
1117A ALA* 3.6 39.9 - - + -
1120A MET* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1081 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A ALA* 4.8 1.0 - - - +
842A LEU* 3.6 15.8 + - + -
843A ARG* 2.8 63.3 + - + +
1079A PRO* 3.5 16.1 - - - +
1080A TRP* 1.3 94.3 + - + +
1082A LEU* 1.3 58.9 + - - +
1085A THR* 2.8 31.0 + - - +
1120A MET* 3.8 31.7 - - + +
1222A LEU* 3.4 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1082 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A GLU* 4.1 8.1 - - - +
735A ILE* 4.3 11.9 - - + -
752A ARG* 3.6 44.6 + - + +
753A VAL* 5.7 4.5 - - + -
842A LEU* 3.8 23.3 - - + -
1037A ALA* 5.5 0.2 - - + -
1078A SER* 4.6 2.7 - - - -
1079A PRO* 3.2 30.6 + - + +
1080A TRP 3.1 0.4 - - - -
1081A GLU* 1.3 79.1 - - - +
1083A GLY* 1.3 57.2 + - - +
1085A THR* 3.3 4.6 - - + +
1086A GLU* 3.1 30.7 + - - +
1221A CYS* 3.7 32.5 - - + -
1222A LEU* 4.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1083 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A ALA* 3.7 21.1 - - - +
1038A GLU 5.2 0.7 - - - -
1041A ILE* 4.1 12.3 - - - -
1058A ILE* 3.8 10.8 - - - -
1079A PRO 3.2 4.9 + - - -
1080A TRP 2.9 5.6 + - - -
1082A LEU* 1.3 77.4 - - - +
1084A VAL* 1.3 59.1 + - - +
1086A GLU* 3.4 1.6 + - - +
1087A VAL* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1084 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A ILE* 4.0 27.1 - - + -
1080A TRP* 2.7 35.3 + - + +
1081A GLU 4.6 0.9 - - - +
1083A GLY* 1.3 68.4 - - - -
1085A THR* 1.3 61.0 + - - +
1087A VAL* 3.4 1.0 + - - +
1088A HIS* 2.8 33.3 + - - +
1102A LEU* 4.5 2.3 - - + +
1104A ALA* 3.7 27.8 - - + -
1117A ALA 4.3 0.7 - - - +
1120A MET* 3.3 31.0 - - + +
1121A GLY 4.2 2.2 - - - -
1122A ALA* 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1085 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A ARG* 5.6 1.3 - - - +
1081A GLU 2.8 23.9 + - - +
1082A LEU* 3.3 10.8 - - + +
1084A VAL* 1.3 80.9 - - - +
1086A GLU* 1.3 59.7 + - + +
1088A HIS* 3.8 0.3 - - - +
1089A ARG* 3.0 33.2 + - - +
1120A MET* 3.8 20.3 - - - +
1221A CYS* 3.3 24.3 + - + +
1222A LEU* 3.7 17.7 - - + +
1225A LEU* 3.7 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1086 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A ARG* 2.9 29.8 + - - +
1038A GLU 3.7 3.6 - - - +
1039A ILE* 3.6 15.4 - - - +
1040A GLY* 3.0 20.5 + - - -
1041A ILE* 3.7 6.0 - - + +
1042A GLY* 2.8 30.9 + - - +
1043A THR 4.5 0.7 + - - -
1082A LEU 3.1 15.3 + - - +
1083A GLY 3.8 2.5 - - - +
1085A THR* 1.3 79.3 - - + +
1087A VAL* 1.3 66.3 + - - +
1089A ARG* 3.8 6.6 - - - +
1090A VAL* 3.0 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1087 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041A ILE* 3.7 33.2 - - + +
1042A GLY* 4.2 5.2 - - - -
1045A ALA* 3.5 27.1 - - + -
1056A ILE* 4.9 2.7 - - + -
1058A ILE* 4.0 18.2 - - + -
1083A GLY 2.9 21.1 + - - +
1086A GLU* 1.3 74.2 - - - +
1088A HIS* 1.3 64.0 + - - +
1090A VAL* 3.9 0.5 - - - +
1091A LEU* 2.9 42.0 + - + +
1102A LEU* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1088 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084A VAL 2.8 21.7 + - - +
1085A THR 3.8 2.7 - - - +
1087A VAL* 1.3 72.2 - - - +
1089A ARG* 1.3 65.2 + - - +
1091A LEU* 3.9 1.2 - - - +
1092A MET* 3.0 58.7 + - + +
1097A ARG* 3.0 33.6 + - - +
1102A LEU* 4.0 13.2 - - + +
1120A MET 3.8 10.5 - - - +
1121A GLY* 4.1 11.5 - - - -
1198A GLY* 4.1 14.0 + - - -
1225A LEU* 4.1 27.1 - - + -
1226A PRO* 4.8 3.3 + - + +
1228A THR* 4.7 0.4 + - - -
1234A TRP* 3.7 25.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1089 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085A THR* 3.0 17.4 + - - +
1086A GLU* 3.8 6.9 - - - +
1088A HIS* 1.3 79.9 - - - +
1090A VAL* 1.3 63.2 + - + +
1092A MET* 3.3 1.4 + - - +
1093A GLU* 2.9 47.1 + - + +
1220A ASP 3.9 0.6 + - - -
1221A CYS* 2.9 38.2 + - - +
1224A ASN* 2.2 39.1 + - - +
1225A LEU* 3.4 14.4 - - + +
1226A PRO* 4.3 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1090 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A THR 5.5 0.2 - - - +
1042A GLY* 3.3 38.1 - - - +
1043A THR* 4.1 7.0 - - - +
1046A ALA* 4.2 8.1 - - + +
1086A GLU* 3.0 29.3 + - + +
1087A VAL 4.1 0.7 - - - +
1089A ARG* 1.3 81.5 - - + +
1091A LEU* 1.3 64.0 + - - +
1093A GLU* 3.4 4.7 + - - +
1094A ASN* 2.9 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1091 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045A ALA* 3.8 22.4 - - + +
1046A ALA* 3.9 11.9 - - - +
1049A ALA* 3.8 9.9 - - + -
1056A ILE* 4.4 2.2 - - + -
1087A VAL* 2.9 40.8 + - + +
1090A VAL* 1.3 74.3 - - + +
1092A MET* 1.3 64.8 + - - +
1094A ASN* 3.3 2.6 + - - -
1095A GLN 3.1 3.5 + - - -
1096A LEU* 2.8 48.9 + - + +
1097A ARG* 3.8 26.9 - - - -
1100A VAL* 3.5 28.5 - - + -
1102A LEU* 3.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1092 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088A HIS* 3.0 44.6 + - + +
1089A ARG 3.6 3.6 - - - +
1091A LEU* 1.3 76.0 - - - +
1093A GLU* 1.3 67.5 + - - +
1095A GLN* 3.1 17.9 + - - +
1097A ARG* 3.7 27.1 - - + +
1226A PRO* 4.0 30.1 - - + +
1227A ASP 4.7 3.4 - - - +
1228A THR* 3.5 24.5 - - - +
1231A ASN 5.3 0.2 - - - +
1234A TRP* 3.8 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1093 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A MET* 3.1 22.5 - - + +
1089A ARG* 2.9 35.3 + - + +
1090A VAL* 4.0 5.8 - - - +
1092A MET* 1.3 80.0 - - - +
1094A ASN* 1.3 60.3 + - - +
1095A GLN* 3.3 5.4 + - - +
1226A PRO* 3.5 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1094 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 4.1 0.3 - - - +
209A THR 4.6 0.4 + - - -
210A ASN* 3.3 17.3 - - - +
211A THR* 2.7 64.0 + - - +
212A MET* 3.4 13.0 - - - +
1046A ALA* 4.2 6.1 - - - +
1090A VAL* 2.9 43.2 + - - +
1091A LEU 3.9 1.1 - - - +
1092A MET 3.2 0.2 - - - -
1093A GLU* 1.3 76.1 - - - +
1095A GLN* 1.3 68.4 + - - +
1096A LEU* 3.3 19.5 + - + +
----------------------------------------------------------
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