Contacts of the helix formed by residues 1092 - 1107 (chain D) in PDB entry 4DAJ
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 ASP1092 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090D SER 4.2 0.8 + - - -
1091D LEU* 1.3 73.0 - - - +
1093D ALA* 1.3 66.0 + - - +
1094D VAL* 3.0 30.7 + - - +
1095D ARG* 2.8 48.0 + - - +
1096D ARG* 2.7 22.0 + - - +
1126D TRP* 5.0 0.7 - - - -
1156D GLY 4.0 4.1 - - - +
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Residues in contact with ALA1093 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D GLU* 6.4 2.2 - - + -
485D GLU* 5.1 7.2 - - - +
1092D ASP* 1.3 71.8 - - - +
1094D VAL* 1.3 65.3 + - + +
1096D ARG* 3.3 19.7 - - - +
1097D ALA* 2.9 25.1 + - - +
1158D TRP* 4.8 3.1 - - + -
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Residues in contact with VAL1094 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D GLU* 3.6 15.5 - - - +
1092D ASP* 3.0 10.9 + - - +
1093D ALA* 1.3 74.0 - - + +
1095D ARG* 1.3 64.4 + - - +
1097D ALA* 2.8 17.0 + - - +
1098D ALA* 3.0 10.6 + - - +
1152D THR* 3.4 26.7 - - + +
1156D GLY 3.2 30.7 - - - +
1157D THR* 3.7 9.9 - - - +
1158D TRP* 3.3 39.5 - - + +
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Residues in contact with ARG1095 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091D LEU* 3.5 24.3 - - + +
1092D ASP* 2.8 39.9 + - - +
1094D VAL* 1.3 78.7 - - - +
1096D ARG* 1.3 63.7 + - - +
1098D ALA* 3.0 11.1 + - - +
1099D LEU 2.9 18.7 + - - -
1126D TRP* 3.3 58.6 - - - +
1152D THR* 4.0 10.5 - - - +
1153D PHE* 2.7 29.2 + - + +
1154D ARG 2.7 27.7 + - - -
1155D THR 4.0 2.8 + - - -
1156D GLY* 3.8 13.2 - - - +
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Residues in contact with ARG1096 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088D TYR* 3.5 41.1 + - + +
1089D ASP* 3.3 21.0 + - - +
1091D LEU* 2.5 40.3 + - + +
1092D ASP* 2.7 23.0 + - - +
1093D ALA* 3.3 18.1 - - - +
1095D ARG* 1.3 72.5 - - - +
1097D ALA* 1.3 64.1 + - - +
1099D LEU* 2.9 7.2 + - - +
1100D ILE* 2.9 26.8 + - + +
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Residues in contact with ALA1097 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003D ILE* 4.2 22.7 - - + +
1006D MET* 3.9 9.3 - - - +
1093D ALA 2.9 11.9 + - - +
1094D VAL 2.8 12.4 + - - +
1096D ARG* 1.3 75.5 - - - +
1098D ALA* 1.3 55.0 + - - +
1100D ILE* 3.4 10.4 + - - +
1101D ASN* 2.9 27.7 + - - +
1158D TRP* 3.5 29.6 - - + -
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Residues in contact with ALA1098 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006D MET* 3.7 13.6 - - + +
1094D VAL 3.0 5.3 + - - -
1095D ARG* 3.0 13.0 + - - +
1097D ALA* 1.3 77.4 - - - +
1099D LEU* 1.3 63.0 + - - +
1101D ASN* 3.0 5.4 + - - +
1102D MET* 3.0 24.4 + - - +
1149D VAL* 3.8 15.7 - - + +
1152D THR* 4.0 15.3 - - + -
1153D PHE* 3.5 26.5 - - + -
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Residues in contact with LEU1099 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078D ILE* 4.3 9.9 - - + -
1084D LEU* 4.3 8.5 - - + +
1087D VAL* 4.5 5.8 - - + -
1088D TYR* 3.7 37.9 - - + +
1091D LEU* 3.5 23.8 - - + -
1095D ARG 2.9 11.0 + - - +
1096D ARG 2.9 9.4 + - - +
1098D ALA* 1.3 75.0 - - - +
1100D ILE* 1.3 57.8 + - - +
1102D MET* 3.0 10.9 + - + +
1103D VAL* 2.9 34.6 + - + +
1111D VAL* 4.8 12.8 - - + -
1118D LEU* 4.7 19.7 - - + -
1121D LEU* 5.5 2.9 - - + -
1153D PHE* 3.7 12.7 - - + -
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Residues in contact with ILE1100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D GLU* 6.1 3.4 - - + -
1003D ILE* 4.6 24.9 - - + -
1007D LEU* 5.4 4.0 - - + -
1071D VAL* 5.0 2.9 - - + +
1074D ALA* 4.2 15.5 - - + -
1075D VAL* 4.0 25.6 - - + -
1078D ILE* 3.5 12.6 - - + -
1088D TYR* 3.3 38.8 - - + +
1096D ARG* 2.9 19.5 + - + +
1097D ALA* 3.6 10.3 - - - +
1099D LEU* 1.3 71.4 - - - +
1101D ASN* 1.3 56.4 + - - +
1103D VAL* 4.0 1.6 - - - +
1104D PHE* 2.9 28.4 + - + +
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Residues in contact with ASN1101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006D MET* 3.0 26.1 - - + +
1007D LEU* 3.5 28.2 - - + +
1010D ASP* 2.8 30.9 + - - -
1097D ALA 2.9 8.4 + - - +
1098D ALA 3.1 9.9 - - - +
1100D ILE* 1.3 74.7 - - - +
1102D MET* 1.3 70.2 + - - +
1104D PHE* 3.1 4.5 + - - +
1105D GLN* 2.9 21.7 + - - +
1138D TRP* 5.3 0.3 - - - -
1145D ARG* 3.4 18.7 + - - +
1149D VAL* 3.7 13.5 - - - +
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Residues in contact with MET1102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098D ALA 3.0 14.4 + - - +
1099D LEU* 3.0 10.8 + - + +
1101D ASN* 1.3 78.7 + - - +
1103D VAL* 1.3 58.1 + - - +
1105D GLN* 3.3 7.0 + - - +
1106D MET* 2.9 48.6 + - + +
1111D VAL* 3.5 27.0 - - + +
1114D PHE* 4.4 12.8 - - + -
1133D LEU* 5.0 9.0 - - + -
1138D TRP* 3.4 44.2 - - + -
1149D VAL* 3.8 5.6 - - + -
1153D PHE* 3.8 26.7 - - - -
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Residues in contact with VAL1103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074D ALA* 3.5 36.5 - - + +
1077D GLY* 5.1 1.6 - - - -
1078D ILE* 4.0 14.8 - - + +
1084D LEU* 3.8 23.6 - - + -
1099D LEU* 2.9 22.3 + - + +
1100D ILE* 4.0 3.4 - - - +
1102D MET* 1.3 74.4 - - - +
1104D PHE* 1.3 63.0 + - - +
1105D GLN 3.0 1.6 - - - -
1107D GLY* 2.9 27.8 + - - +
1108D GLU* 4.7 11.9 - - + +
1111D VAL* 3.6 25.4 - - + -
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Residues in contact with PHE1104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007D LEU* 4.0 28.9 - - + -
1011D GLU* 4.0 1.6 - - + -
1029D ILE* 3.6 8.3 - - + -
1030D GLY* 3.3 49.6 - - - +
1067D PHE* 4.7 7.6 - + - -
1070D ASP* 3.4 43.5 - - + -
1071D VAL* 4.5 4.3 - - - -
1074D ALA* 3.8 11.7 - - + -
1100D ILE* 2.9 21.7 + - + +
1101D ASN* 3.4 5.2 - - - +
1103D VAL* 1.3 75.9 - - - +
1105D GLN* 1.3 64.1 + - - +
1107D GLY 4.8 0.4 + - - -
1145D ARG* 3.8 22.7 - - - -
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Residues in contact with GLN1105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011D GLU* 5.5 0.7 - - - +
1022D GLU* 5.3 5.5 + - - -
1030D GLY 6.0 0.2 - - - -
1032D LEU* 5.7 4.3 - - - +
1101D ASN* 2.9 13.4 + - - +
1102D MET* 3.5 7.4 - - - +
1104D PHE* 1.3 83.8 - - - +
1106D MET* 1.3 71.0 + - + +
1107D GLY 3.4 0.6 + - - -
1138D TRP* 3.0 40.2 + - - +
1142D THR* 4.2 10.9 + - - +
1145D ARG* 3.2 43.2 + - - +
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Residues in contact with MET1106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102D MET* 2.9 41.3 + - + +
1105D GLN* 1.3 87.8 - - + +
1107D GLY* 1.3 61.4 + - - +
1110D GLY* 3.8 12.5 + - - -
1111D VAL* 3.9 11.7 - - + +
1114D PHE* 3.6 36.3 - - + -
1138D TRP* 3.9 33.7 - - + -
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Residues in contact with GLY1107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103D VAL 2.9 18.7 + - - -
1104D PHE 4.8 0.2 - - - -
1105D GLN 3.4 2.4 - - - -
1106D MET* 1.3 76.8 - - - +
1108D GLU* 1.3 61.2 + - - -
1109D THR* 3.4 2.9 - - - -
1110D GLY 2.9 3.3 + - - -
1111D VAL* 2.9 29.0 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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