Contacts of the helix formed by residues 1090 - 1104 (chain A) in PDB entry 4DDG
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 ASN1090 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088A ASP* 3.3 8.9 + - - +
1089A GLY* 1.3 78.0 - - - +
1091A SER* 1.3 62.3 - - - +
1092A PHE 3.0 5.0 + - - -
1093A TYR* 3.0 17.4 + - - -
1094A ARG* 3.0 38.9 + - - +
1169A ASP* 4.9 0.4 + - - -
1172A VAL* 3.7 18.8 - - + -
1176A ARG* 2.7 31.8 + - - +
1211A MET* 3.3 27.6 - - - +
1212A CYS* 3.0 26.5 + - - +
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Residues in contact with SER1091 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085A THR* 3.5 15.5 + - - -
1086A ARG 3.3 23.6 - - - -
1087A PRO* 4.9 1.8 - - - -
1088A ASP* 3.5 3.9 + - - -
1089A GLY* 3.4 5.0 + - - -
1090A ASN* 1.3 77.1 - - - +
1092A PHE* 1.3 58.1 + - - +
1094A ARG* 3.7 5.7 - - - +
1095A ALA* 2.9 33.4 + - - +
1264A GLY 5.1 0.9 + - - -
1265A HIS* 3.6 14.4 + - - -
1266A TYR* 3.5 24.8 + - - +
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Residues in contact with PHE1092 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089A GLY 5.2 0.4 + - - -
1090A ASN 3.0 1.0 + - - -
1091A SER* 1.3 81.1 + - - +
1093A TYR* 1.3 77.2 + + + +
1095A ALA* 3.9 0.7 - - - +
1096A PHE* 2.9 50.3 + + - +
1215A SER* 3.3 28.7 - - - +
1219A HIS 4.5 2.2 - - - -
1220A ILE* 3.5 55.0 - - + -
1223A LEU* 4.0 21.8 - - + -
1259A LEU* 4.2 17.7 - - + -
1266A TYR* 3.6 37.2 - + + -
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Residues in contact with TYR1093 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089A GLY 5.3 0.2 - - - -
1090A ASN* 3.0 12.1 + - - +
1092A PHE* 1.3 88.5 - + + +
1094A ARG* 1.3 58.8 + - - +
1096A PHE* 3.9 3.3 - - - +
1097A GLY* 2.9 23.9 + - - -
1171A LEU* 4.5 0.3 - - - +
1172A VAL* 4.0 14.8 - - + -
1175A LEU* 3.4 30.6 - - + +
1176A ARG* 3.3 56.8 + - + +
1179A THR* 3.4 26.5 - - + +
1208A VAL* 4.4 2.3 - - - +
1215A SER* 3.9 17.7 - - - -
1219A HIS* 2.9 34.4 - + + +
1223A LEU* 3.9 16.4 - - + -
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Residues in contact with ARG1094 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047A LEU* 3.5 41.5 - - - +
1048A VAL* 4.3 12.6 - - + -
1085A THR* 4.7 7.4 - - + -
1086A ARG* 5.0 1.9 - - - +
1088A ASP* 2.6 36.9 + - - -
1090A ASN* 3.0 31.9 + - - +
1091A SER* 3.7 6.1 - - - +
1093A TYR* 1.3 78.4 - - - +
1095A ALA* 1.3 57.6 + - - +
1097A GLY* 3.9 0.3 - - - -
1098A PHE* 3.0 32.6 + - - +
1162A PHE* 4.0 9.3 - - + -
1165A GLN* 5.7 0.2 - - - +
1168A SER* 2.4 39.9 + - - +
1169A ASP* 3.3 25.2 + - - -
1171A LEU* 5.1 0.4 - - - -
1172A VAL* 3.8 16.3 - - + +
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Residues in contact with ALA1095 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085A THR* 4.1 13.6 - - + +
1091A SER 2.9 18.6 + - - +
1092A PHE* 3.9 3.6 - - - +
1094A ARG* 1.3 73.8 - - - +
1096A PHE* 1.3 64.1 + - - +
1098A PHE* 3.3 0.6 + - - -
1099A SER* 2.8 34.0 + - - -
1259A LEU* 3.9 13.2 - - + -
1266A TYR* 5.0 2.7 - - + -
1267A ASP* 4.6 7.2 - - - -
1268A ILE* 3.7 27.1 - - + +
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Residues in contact with PHE1096 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A PHE* 2.9 46.1 + + + +
1093A TYR* 3.9 3.6 - - - +
1095A ALA* 1.3 70.8 - - - +
1097A GLY* 1.3 69.0 + - - +
1099A SER* 3.2 5.9 + - - -
1100A HIS* 2.9 40.7 + + + +
1175A LEU* 4.8 3.8 - - + -
1220A ILE* 5.3 1.3 - - + -
1223A LEU* 3.5 35.0 - - + -
1224A ALA* 4.5 11.2 - - + -
1227A LEU* 3.6 21.5 - - + -
1229A VAL* 3.8 24.7 - - + -
1231A ILE* 3.5 36.6 - - + -
1259A LEU* 4.4 6.8 - - + +
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Residues in contact with GLY1097 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A TYR 2.9 18.0 + - - -
1094A ARG 3.9 0.2 - - - -
1096A PHE* 1.3 82.2 - - - +
1098A PHE* 1.3 61.7 + - - +
1100A HIS* 3.3 2.0 + - - +
1101A LEU* 3.0 30.4 + - - +
1142A PHE* 6.3 1.6 - - - -
1162A PHE* 4.0 9.2 - - - -
1171A LEU* 4.8 3.4 - - - -
1175A LEU* 4.1 15.5 - - - -
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Residues in contact with PHE1098 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048A VAL* 4.5 10.8 - - + -
1083A ARG* 3.4 36.3 - - - -
1094A ARG 3.0 19.5 + - - +
1095A ALA* 4.0 1.6 - - - +
1097A GLY* 1.3 75.0 - - - +
1099A SER* 1.3 60.4 + - - +
1101A LEU* 3.8 1.4 - - - +
1102A GLU* 2.9 55.2 + - - +
1155A VAL* 4.6 2.5 - - + -
1158A LEU* 3.6 28.4 - - + +
1159A LEU* 3.6 26.0 - - + -
1162A PHE* 3.4 42.6 - + + -
1268A ILE* 3.6 17.7 - - + -
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Residues in contact with SER1099 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A ALA 2.8 23.2 + - - -
1096A PHE* 3.2 4.3 + - - -
1098A PHE* 1.3 82.6 - - - +
1100A HIS* 1.3 59.3 + - - +
1102A GLU* 3.8 8.9 - - - +
1103A ALA* 2.9 27.7 + - - +
1257A VAL* 3.2 27.6 - - - +
1258A TYR 5.6 0.2 - - - -
1259A LEU* 4.1 3.5 - - - +
1268A ILE* 3.7 28.0 - - - -
1270A TYR* 5.7 0.7 - - - -
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Residues in contact with HIS1100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096A PHE* 2.9 37.1 + + + +
1097A GLY* 4.0 2.9 - - - +
1099A SER* 1.3 76.8 + - - +
1101A LEU* 1.3 62.7 + - + +
1103A ALA* 3.6 5.3 - - + +
1104A LEU* 3.1 38.8 - - + +
1114A PHE* 4.9 11.4 - + + -
1229A VAL* 3.1 44.0 - - + +
1230A SER* 3.0 30.0 + - - -
1231A ILE* 4.2 4.9 - - + -
1257A VAL* 3.8 28.6 - - + +
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Residues in contact with LEU1101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097A GLY* 3.0 18.3 + - - +
1098A PHE 3.8 2.7 - - - +
1100A HIS* 1.3 73.7 - - - +
1102A GLU* 1.3 60.9 + - - +
1103A ALA 3.0 1.6 - - - -
1104A LEU* 2.9 28.7 + - + +
1105A LEU 3.0 8.8 + - - -
1114A PHE* 3.8 31.4 - - + -
1142A PHE* 5.2 3.6 - - + -
1145A LEU* 3.9 34.3 - - + +
1146A ILE* 4.3 17.5 - - + -
1149A VAL* 3.4 16.7 - - + +
1158A LEU* 3.9 12.3 - - + -
1162A PHE* 4.1 21.8 - - + -
1171A LEU* 4.7 7.2 - - + -
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Residues in contact with GLU1102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051A ARG* 4.7 4.3 + - - -
1083A ARG* 3.5 13.2 + - - -
1098A PHE* 2.9 33.0 + - + +
1099A SER* 3.8 6.9 - - - +
1101A LEU* 1.3 76.9 - - - +
1103A ALA* 1.3 61.0 + - - +
1105A LEU* 3.1 25.2 - - - +
1106A ASP* 4.1 4.9 - - - +
1155A VAL* 3.3 35.2 - - + +
1158A LEU* 4.5 6.8 - - + +
1270A TYR* 2.3 44.0 + - - -
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Residues in contact with ALA1103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099A SER 2.9 18.6 + - - +
1100A HIS* 3.6 9.6 - - + +
1101A LEU 3.0 0.2 - - - -
1102A GLU* 1.3 78.6 - - - +
1104A LEU* 1.3 65.4 + - + +
1105A LEU 3.2 0.9 + - - -
1106A ASP* 3.5 19.8 - - - +
1107A ASP* 4.3 4.2 + - - +
1256A LYS* 5.1 8.3 - - + +
1257A VAL* 3.7 21.3 - - + -
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Residues in contact with LEU1104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100A HIS* 3.1 32.8 - - + +
1101A LEU* 2.9 19.8 + - + +
1103A ALA* 1.3 78.6 - - + +
1105A LEU* 1.3 61.4 + - - +
1106A ASP 2.9 7.8 + - - +
1107A ASP* 3.6 14.1 - - - +
1110A GLU* 3.8 27.6 - - + +
1111A LEU* 3.5 47.0 - - + +
1114A PHE* 3.7 40.6 - - + -
1146A ILE* 5.4 0.7 - - + -
1149A VAL* 4.2 4.5 - - + -
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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
------------------------------------------------------------
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