Contacts of the helix formed by residues 1090 - 1104 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088B ASP* 3.3 9.3 + - - +
1089B GLY* 1.3 78.0 - - - +
1091B SER* 1.3 63.3 + - - +
1092B PHE 3.0 4.6 + - - -
1093B TYR* 3.0 17.1 + - - +
1094B ARG* 3.0 37.9 + - - +
1169B ASP* 4.9 0.4 + - - -
1172B VAL* 3.7 18.2 - - + -
1176B ARG* 2.7 32.9 + - - +
1211B MET* 3.3 27.0 - - - +
1212B CYS* 3.0 25.9 + - - +
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Residues in contact with SER1091 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085B THR* 3.5 16.1 + - - -
1086B ARG 3.3 23.8 - - - -
1087B PRO* 4.9 1.8 - - - -
1088B ASP* 3.5 3.5 + - - -
1089B GLY 3.4 4.1 + - - -
1090B ASN* 1.3 76.2 - - - +
1092B PHE* 1.3 59.8 + - - +
1094B ARG* 3.7 5.9 - - - +
1095B ALA* 2.9 32.4 + - - +
1264B GLY 5.1 0.9 + - - -
1265B HIS* 3.6 14.3 + - - -
1266B TYR* 3.5 26.0 + - - +
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Residues in contact with PHE1092 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089B GLY 5.2 0.4 + - - -
1090B ASN 3.0 1.2 + - - -
1091B SER* 1.3 81.3 + - - +
1093B TYR* 1.3 77.5 + + + +
1095B ALA* 3.9 1.0 - - - +
1096B PHE* 2.9 52.0 + + - +
1215B SER* 3.3 28.3 - - - +
1219B HIS 4.5 2.9 - - - -
1220B ILE* 3.5 55.4 - - + -
1223B LEU* 4.0 21.1 - - + -
1259B LEU* 4.2 18.6 - - + -
1266B TYR* 3.6 37.4 - + + -
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Residues in contact with TYR1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089B GLY 5.3 0.2 - - - -
1090B ASN* 3.0 11.9 + - - +
1092B PHE* 1.3 90.9 - + + +
1094B ARG* 1.3 57.5 + - - +
1096B PHE* 4.4 3.4 - - - -
1097B GLY* 2.9 24.4 + - - -
1171B LEU* 4.5 0.3 - - - +
1172B VAL* 4.0 14.8 - - + -
1175B LEU* 3.4 30.7 - - + +
1176B ARG* 3.3 55.9 + - + +
1179B THR* 3.4 25.8 - - + +
1208B VAL* 4.4 1.9 - - - +
1215B SER* 3.9 17.7 - - - -
1219B HIS* 2.9 34.1 - + + +
1223B LEU* 3.9 16.2 - - + -
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Residues in contact with ARG1094 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047B LEU* 3.5 41.3 - - - +
1048B VAL* 4.3 13.0 - - + -
1085B THR* 4.7 7.6 - - + -
1086B ARG* 5.0 1.9 - - - +
1088B ASP* 2.6 36.2 + - - -
1090B ASN* 3.0 32.6 + - - +
1091B SER* 3.7 5.8 - - - +
1093B TYR* 1.3 78.4 - - - +
1095B ALA* 1.3 57.4 - - - +
1097B GLY* 3.9 0.2 - - - -
1098B PHE* 3.0 31.9 + - - +
1162B PHE* 4.0 9.8 - - + -
1168B SER* 2.4 40.8 + - - +
1169B ASP* 3.3 24.2 + - - -
1171B LEU* 5.1 0.7 - - - -
1172B VAL* 3.8 15.7 - - + +
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Residues in contact with ALA1095 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085B THR* 4.1 13.8 - - + +
1091B SER 2.9 19.2 + - - +
1092B PHE* 3.9 3.8 - - - +
1094B ARG* 1.3 74.0 - - - +
1096B PHE* 1.3 63.4 + - - +
1098B PHE* 3.3 0.6 + - - -
1099B SER* 2.8 33.4 + - - -
1259B LEU* 3.9 13.5 - - + -
1266B TYR* 5.0 3.1 - - + -
1267B ASP* 4.6 7.4 - - - -
1268B ILE* 3.7 27.1 - - + +
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Residues in contact with PHE1096 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092B PHE* 2.9 46.8 + + + +
1093B TYR* 3.9 3.4 - - - +
1095B ALA* 1.3 72.1 - - - +
1097B GLY* 1.3 68.7 + - - +
1099B SER* 3.2 5.5 + - - -
1100B HIS* 2.9 41.4 + + + +
1175B LEU* 4.8 4.5 - - + -
1220B ILE 5.3 0.9 - - - -
1223B LEU* 3.5 33.9 - - + -
1224B ALA* 4.5 11.4 - - + -
1227B LEU* 3.7 21.8 - - + -
1229B VAL* 3.8 25.1 - - + -
1231B ILE* 3.5 36.8 - - + -
1259B LEU* 4.4 6.6 - - + +
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Residues in contact with GLY1097 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093B TYR 2.9 18.3 + - - -
1094B ARG 3.9 0.7 - - - -
1096B PHE* 1.3 82.3 - - - +
1098B PHE* 1.3 61.6 + - - +
1100B HIS* 3.8 2.4 - - - +
1101B LEU* 3.0 29.7 + - - +
1142B PHE* 6.3 1.3 - - - -
1162B PHE* 4.0 9.0 - - - -
1171B LEU* 4.8 3.4 - - - -
1175B LEU* 4.1 15.3 - - - -
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Residues in contact with PHE1098 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048B VAL* 4.5 10.3 - - + -
1083B ARG* 3.4 36.1 - - - -
1094B ARG 3.0 18.5 + - - +
1095B ALA* 4.0 2.0 - - - +
1097B GLY* 1.3 75.1 - - - +
1099B SER* 1.3 61.0 + - - +
1101B LEU* 3.3 1.9 + - - +
1102B GLU* 2.9 56.0 + - - +
1155B VAL* 4.6 2.2 - - + -
1158B LEU* 3.6 21.7 - - + +
1159B LEU* 3.6 31.6 - - + -
1162B PHE* 3.4 43.4 - + + -
1268B ILE* 3.6 17.9 - - + -
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Residues in contact with SER1099 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095B ALA 2.8 23.0 + - - -
1096B PHE* 3.2 4.7 + - - -
1098B PHE* 1.3 83.0 - - - +
1100B HIS* 1.3 59.4 + - - +
1102B GLU* 3.8 7.8 - - - +
1103B ALA* 2.9 28.2 + - - +
1257B VAL* 3.2 28.3 - - - +
1259B LEU* 4.1 3.3 - - - +
1268B ILE* 3.7 28.3 - - - -
1270B TYR* 5.7 0.2 - - - -
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Residues in contact with HIS1100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096B PHE* 2.9 36.4 + + + +
1097B GLY* 4.0 3.4 - - - +
1099B SER* 1.3 78.1 + - - +
1101B LEU* 1.3 61.2 + - - +
1103B ALA* 3.6 4.6 - - + +
1104B LEU* 3.1 39.6 - - + +
1114B PHE* 4.9 11.8 - + + -
1229B VAL* 3.1 42.9 - - + +
1230B SER* 3.0 30.8 + - - -
1231B ILE* 4.2 5.6 - - + -
1257B VAL* 3.8 28.0 - - + +
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Residues in contact with LEU1101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097B GLY* 3.0 18.5 + - - +
1098B PHE 3.8 2.7 - - - +
1100B HIS* 1.3 73.9 - - + +
1102B GLU* 1.3 60.5 + - - +
1103B ALA 3.0 1.6 - - - -
1104B LEU* 2.9 28.2 + - + +
1105B LEU 3.0 9.0 + - - -
1114B PHE* 3.8 31.2 - - + -
1142B PHE* 5.2 4.5 - - + -
1145B LEU* 3.9 33.9 - - + +
1146B ILE* 4.3 15.7 - - + -
1149B VAL* 3.4 17.2 - - + +
1158B LEU* 3.9 13.0 - - + -
1162B PHE* 4.1 20.9 - - + -
1171B LEU* 4.7 7.0 - - + -
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Residues in contact with GLU1102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051B ARG* 4.7 4.5 + - - -
1083B ARG* 3.5 13.2 + - - -
1098B PHE* 2.9 32.7 + - + +
1099B SER* 3.8 7.1 - - - +
1101B LEU* 1.3 75.8 - - - +
1103B ALA* 1.3 62.2 + - - +
1105B LEU* 3.1 24.9 - - - +
1106B ASP* 4.1 4.7 - - - +
1155B VAL* 3.3 35.2 - - + +
1158B LEU* 4.5 7.7 - - + +
1270B TYR* 2.3 44.1 + - - -
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Residues in contact with ALA1103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099B SER 2.9 19.9 + - - +
1100B HIS* 3.6 9.4 - - + +
1101B LEU 3.0 0.2 - - - -
1102B GLU* 1.3 78.9 - - - +
1104B LEU* 1.3 64.4 + - + +
1105B LEU 3.4 0.9 + - - -
1106B ASP* 3.5 19.3 - - - +
1107B ASP* 4.3 4.5 + - - +
1256B LYS* 5.1 9.0 - - + +
1257B VAL* 3.7 20.9 - - + -
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Residues in contact with LEU1104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100B HIS* 3.1 33.0 - - + +
1101B LEU* 2.9 18.7 + - + +
1103B ALA* 1.3 78.4 - - + +
1105B LEU* 1.3 59.9 + - - +
1106B ASP 2.9 8.1 + - - +
1107B ASP* 3.6 13.9 - - - +
1110B GLU* 3.8 28.0 - - + +
1111B LEU* 3.5 46.4 - - + +
1114B PHE* 3.7 41.3 - - + -
1146B ILE* 5.4 0.9 - - + -
1149B VAL* 4.2 4.9 - - + -
1229B VAL* 6.1 0.7 - - + -
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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
------------------------------------------------------------
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