Contacts of the helix formed by residues 1090 - 1104 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088C ASP* 3.3 8.9 + - - +
1089C GLY* 1.3 77.9 - - - +
1091C SER* 1.3 63.1 + - - +
1092C PHE 3.0 4.7 + - - -
1093C TYR* 3.0 16.8 + - - +
1094C ARG* 3.1 38.7 + - - +
1169C ASP* 4.9 0.6 + - - -
1172C VAL* 3.7 17.7 - - + +
1176C ARG* 2.7 32.7 + - - +
1211C MET* 3.3 26.6 - - - +
1212C CYS* 3.0 25.6 + - - +
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Residues in contact with SER1091 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085C THR* 3.5 15.9 + - - -
1086C ARG 3.3 23.8 - - - -
1087C PRO* 4.9 1.8 - - - -
1088C ASP* 3.5 3.5 + - - -
1089C GLY* 3.4 5.1 + - - -
1090C ASN* 1.3 76.8 - - - +
1092C PHE* 1.3 58.8 + - - +
1094C ARG* 3.7 5.9 - - - +
1095C ALA* 2.9 32.9 + - - +
1264C GLY 5.1 1.2 + - - -
1265C HIS* 3.6 14.1 + - - -
1266C TYR* 3.5 25.7 + - - +
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Residues in contact with PHE1092 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089C GLY 5.2 0.4 + - - -
1090C ASN 3.0 1.2 + - - -
1091C SER* 1.3 82.8 + - - +
1093C TYR* 1.3 77.2 + + + +
1095C ALA* 3.9 1.0 - - - +
1096C PHE* 2.9 51.1 + + + +
1215C SER* 3.3 28.5 - - - +
1219C HIS 4.5 2.5 - - - -
1220C ILE* 3.5 55.2 - - + -
1223C LEU* 4.0 21.5 - - + -
1259C LEU* 4.2 17.0 - - + -
1266C TYR* 3.6 37.2 - + + -
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Residues in contact with TYR1093 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089C GLY 5.3 0.4 - - - -
1090C ASN* 3.0 12.1 + - - +
1092C PHE* 1.3 90.3 - + + +
1094C ARG* 1.3 58.3 + - - +
1096C PHE* 4.4 3.1 - - - -
1097C GLY* 2.9 24.8 + - - -
1171C LEU* 4.5 0.3 - - - +
1172C VAL* 4.0 15.7 - - + -
1175C LEU* 3.4 31.9 - - + +
1176C ARG* 3.3 57.2 + - + +
1179C THR* 3.4 25.5 - - + +
1208C VAL* 4.4 2.4 - - - +
1215C SER* 3.9 17.7 - - - -
1219C HIS* 2.9 33.6 - + + +
1223C LEU* 3.9 15.7 - - + -
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Residues in contact with ARG1094 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047C LEU* 3.5 41.0 - - - +
1048C VAL* 4.3 12.1 - - + -
1085C THR* 4.7 8.1 - - + -
1086C ARG* 5.0 2.0 - - - +
1088C ASP* 2.6 36.9 + - - -
1090C ASN* 3.1 33.3 + - - +
1091C SER* 3.7 5.8 - - - +
1093C TYR* 1.3 77.8 - - - +
1095C ALA* 1.3 57.4 + - - +
1097C GLY* 3.9 0.2 - - - -
1098C PHE* 3.0 31.9 + - - +
1162C PHE* 4.0 8.9 - - + -
1168C SER* 2.4 40.2 + - - +
1169C ASP* 3.3 24.4 + - - -
1171C LEU* 5.1 0.7 - - - -
1172C VAL* 3.8 16.0 - - + +
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Residues in contact with ALA1095 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085C THR* 4.1 14.1 - - + +
1091C SER 2.9 18.9 + - - +
1092C PHE* 3.9 2.9 - - - +
1094C ARG* 1.3 73.8 - - - +
1096C PHE* 1.3 63.4 + - - +
1098C PHE* 3.3 0.6 + - - -
1099C SER* 2.8 33.1 + - - -
1259C LEU* 3.9 13.7 - - + -
1266C TYR* 5.0 2.7 - - + -
1267C ASP* 4.6 7.6 - - - -
1268C ILE* 3.7 26.4 - - + +
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Residues in contact with PHE1096 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092C PHE* 2.9 46.8 + + + +
1093C TYR* 3.9 3.4 - - - +
1095C ALA* 1.3 72.1 - - - +
1097C GLY* 1.3 69.1 + - - +
1099C SER* 3.2 5.3 + - - -
1100C HIS* 2.9 41.0 + + + +
1175C LEU* 4.8 4.0 - - + -
1220C ILE* 5.3 1.3 - - + -
1223C LEU* 3.5 34.5 - - + -
1224C ALA* 4.5 11.2 - - + -
1227C LEU* 3.7 21.5 - - + -
1229C VAL* 3.8 24.0 - - + -
1231C ILE* 3.5 36.6 - - + -
1259C LEU* 4.4 6.8 - - + +
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Residues in contact with GLY1097 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093C TYR 2.9 18.7 + - - -
1094C ARG 3.9 0.4 - - - -
1096C PHE* 1.3 81.5 - - - +
1098C PHE* 1.3 63.1 + - - +
1100C HIS* 3.8 2.2 - - - +
1101C LEU* 3.0 30.4 + - - +
1142C PHE* 6.3 1.6 - - - -
1162C PHE* 4.0 9.6 - - - -
1171C LEU* 4.8 3.1 - - - -
1175C LEU* 4.1 15.3 - - - -
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Residues in contact with PHE1098 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048C VAL* 4.5 11.0 - - + -
1083C ARG* 3.4 37.5 - - - -
1094C ARG 3.0 17.8 + - - +
1095C ALA* 4.0 2.0 - - - +
1097C GLY* 1.3 74.6 - - - +
1099C SER* 1.3 61.6 + - - +
1101C LEU* 3.3 1.7 + - - +
1102C GLU* 2.9 55.4 + - - +
1155C VAL* 4.6 2.5 - - + -
1158C LEU* 3.6 29.7 - - + +
1159C LEU* 3.6 25.4 - - + -
1162C PHE* 3.4 43.9 - + + -
1268C ILE* 3.6 18.2 - - + -
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Residues in contact with SER1099 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095C ALA 2.8 22.7 + - - -
1096C PHE* 3.2 5.4 + - - -
1098C PHE* 1.3 84.1 - - - +
1100C HIS* 1.3 58.2 + - - +
1102C GLU* 3.8 8.6 - - - +
1103C ALA* 2.9 28.6 + - - +
1257C VAL* 3.2 27.4 - - - +
1258C TYR 5.6 0.2 - - - -
1259C LEU* 4.1 3.5 - - - +
1268C ILE* 3.7 28.5 - - - -
1270C TYR* 5.7 0.4 - - - -
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Residues in contact with HIS1100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096C PHE* 2.9 36.3 + + + +
1097C GLY* 4.0 3.4 - - - +
1099C SER* 1.3 77.7 + - - +
1101C LEU* 1.3 61.0 + - - +
1103C ALA* 3.6 5.1 - - + +
1104C LEU* 3.1 39.5 - - + +
1114C PHE* 4.9 11.6 - + + -
1229C VAL* 3.2 44.2 - - + +
1230C SER* 3.0 31.2 + - - -
1231C ILE* 4.2 5.6 - - + -
1257C VAL* 3.8 27.9 - - + +
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Residues in contact with LEU1101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C GLY* 3.0 18.8 + - - +
1098C PHE 3.8 2.5 - - - +
1100C HIS* 1.3 74.1 - - + +
1102C GLU* 1.3 61.3 + - - +
1103C ALA 3.0 1.6 - - - -
1104C LEU* 2.9 28.9 + - + +
1105C LEU 3.0 8.7 + - - -
1114C PHE* 3.8 31.0 - - + -
1142C PHE* 5.2 4.3 - - + -
1145C LEU* 3.9 34.8 - - + +
1146C ILE* 4.3 16.2 - - + -
1149C VAL* 3.4 16.2 - - + +
1158C LEU* 3.9 12.6 - - + -
1162C PHE* 4.1 20.9 - - + -
1171C LEU* 4.7 7.0 - - + -
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Residues in contact with GLU1102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051C ARG* 4.7 4.7 + - - -
1083C ARG* 3.5 13.5 + - - -
1098C PHE* 2.9 32.5 + - + +
1099C SER* 3.8 7.5 - - - +
1101C LEU* 1.3 76.7 - - - +
1103C ALA* 1.3 60.7 + - - +
1105C LEU* 3.1 25.5 - - - +
1106C ASP* 4.1 4.7 - - - +
1155C VAL* 3.4 36.3 - - + +
1158C LEU* 4.5 7.3 - - + +
1270C TYR* 2.3 43.1 + - - -
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Residues in contact with ALA1103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099C SER 2.9 18.6 + - - +
1100C HIS* 3.6 9.9 - - + +
1101C LEU 3.0 0.4 - - - -
1102C GLU* 1.3 78.6 - - - +
1104C LEU* 1.3 62.7 + - + +
1105C LEU 3.2 1.3 + - - -
1106C ASP* 3.5 20.0 - - - +
1107C ASP* 4.3 4.3 + - - +
1256C LYS* 5.1 8.7 - - + +
1257C VAL* 3.7 21.3 - - + -
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Residues in contact with LEU1104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100C HIS* 3.1 33.4 - - + +
1101C LEU* 2.9 18.9 + - + +
1103C ALA* 1.3 78.4 - - + +
1105C LEU* 1.3 61.0 + - - +
1106C ASP 2.9 7.8 + - - +
1107C ASP* 3.6 13.5 - - - +
1110C GLU* 3.8 27.4 - - + +
1111C LEU* 3.5 45.3 - - + +
1114C PHE* 3.7 42.0 - - + -
1146C ILE* 5.4 0.4 - - + -
1149C VAL* 4.2 4.9 - - + -
1229C VAL* 6.1 0.4 - - + -
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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