Contacts of the helix formed by residues 1181 - 1191 (chain C) in PDB entry 2VE7
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 SER1181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1180C LEU* 1.3 77.5 - - - +
1182C ARG* 1.3 65.9 + - - +
1183C LYS* 4.0 6.6 + - - +
1184C PHE* 3.2 26.8 + - - +
1185C ILE* 3.2 23.1 + - - +
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Residues in contact with ARG1182 (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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1140A ASP* 3.2 56.0 + - - +
1141A ARG 4.7 0.9 - - - +
1160A ASN* 3.7 23.8 + - - +
1167A GLU* 6.2 0.9 - - - -
1180C LEU 4.0 0.4 + - - -
1181C SER* 1.3 73.0 - - - +
1183C LYS* 1.3 57.7 + - - +
1185C ILE* 3.2 14.3 + - + +
1186C SER* 3.0 28.2 + - - -
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Residues in contact with LYS1183 (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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1160A ASN* 3.4 31.6 + - + +
1161A ILE 3.6 33.5 - - - -
1165A ASN* 4.2 25.8 - - + +
1166A PRO 5.5 0.2 - - - +
1219A THR* 5.6 1.8 + - - -
1181C SER* 3.3 6.3 - - - +
1182C ARG* 1.3 75.2 - - - +
1184C PHE* 1.3 59.6 - - - +
1186C SER* 3.7 1.0 - - - -
1187C ASP* 2.9 58.1 + - - +
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Residues in contact with PHE1184 (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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1175C LEU* 4.9 8.5 - - + -
1180C LEU* 3.6 39.3 - - + -
1181C SER* 3.2 29.1 + - - +
1182C ARG 3.3 0.2 - - - -
1183C LYS* 1.3 76.2 - - - +
1185C ILE* 1.3 62.5 + - + +
1187C ASP* 3.5 7.6 + - + +
1188C TYR* 2.9 43.1 + + + +
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Residues in contact with ILE1185 (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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1141A ARG* 4.2 19.7 - - + +
1160C VAL* 4.7 8.5 - - + -
1175C LEU* 3.8 30.1 - - + -
1177C SER* 3.8 34.8 - - - +
1180C LEU* 4.4 11.4 - - + +
1181C SER 3.2 18.4 + - - +
1182C ARG* 3.2 12.6 + - + +
1184C PHE* 1.3 74.3 - - + +
1186C SER* 1.3 65.9 + - - +
1188C TYR* 3.3 2.4 + - - +
1189C LEU* 3.1 43.7 + - + +
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Residues in contact with SER1186 (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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1140A ASP 4.6 0.9 + - - -
1141A ARG 2.9 22.4 + - - -
1142A LEU 3.7 13.6 + - - -
1143A GLY 4.0 0.2 + - - -
1160A ASN* 3.4 20.0 + - - +
1215A ARG* 3.7 18.4 - - - -
1182C ARG 3.0 12.0 + - - -
1183C LYS 3.7 8.5 - - - -
1185C ILE* 1.3 75.8 - - - +
1187C ASP* 1.3 58.4 + - - +
1189C LEU* 3.2 4.3 + - - +
1190C TRP* 3.0 38.8 + - - -
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Residues in contact with ASP1187 (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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1160A ASN 4.3 1.0 - - - +
1215A ARG* 3.3 27.6 + - - +
1183C LYS* 2.9 51.1 + - - +
1184C PHE* 3.8 7.7 - - + +
1186C SER* 1.3 76.4 - - - +
1188C TYR* 1.3 56.7 + - - +
1190C TRP* 3.9 0.9 - - - +
1191C SER* 3.0 30.1 + - - -
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Residues in contact with TYR1188 (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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1171C GLN* 5.2 5.0 + - - -
1172C PRO 5.0 4.9 + - - -
1173C ILE* 3.9 29.9 - - + +
1174C HIS 5.5 0.7 + - - -
1175C LEU* 3.9 35.2 - - + -
1184C PHE* 2.9 34.6 + + + +
1185C ILE* 3.3 5.4 + - - +
1187C ASP* 1.3 76.3 - - - +
1189C LEU* 1.3 67.6 + - + +
1191C SER* 2.7 23.7 + - - -
1192C LEU* 3.3 24.5 - - + +
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Residues in contact with LEU1189 (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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1141A ARG* 3.8 35.4 - - + +
1142A LEU* 3.8 25.6 - - + -
1147C SER 5.6 1.4 - - - +
1149C ILE* 4.4 12.2 - - + +
1151C TRP* 4.0 9.4 - - + -
1160C VAL* 5.9 1.1 - - + -
1164C HIS* 5.6 2.1 - - - -
1173C ILE* 3.8 31.0 - - + -
1175C LEU* 4.6 7.9 - - + -
1185C ILE* 3.1 28.9 + - + +
1186C SER 3.6 2.7 - - - +
1188C TYR* 1.3 90.0 - - + +
1190C TRP* 1.3 61.0 - - - +
1192C LEU* 3.4 21.8 + - + +
1193C VAL* 3.8 5.7 + - - +
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Residues in contact with TRP1190 (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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1142A LEU* 3.2 51.3 + - + +
1144A LEU* 3.5 33.7 - - + -
1158A PHE* 4.7 7.8 - + - -
1215A ARG* 3.2 55.1 - - + +
1216A LYS* 5.9 2.6 - - - -
1146C VAL* 4.9 19.7 - - + -
1147C SER* 5.4 6.3 - - - -
1186C SER 3.0 27.5 + - - +
1187C ASP 4.3 0.9 - - - +
1189C LEU* 1.3 71.2 - - - +
1191C SER* 1.3 61.6 + - - +
1192C LEU 3.1 3.1 - - - -
1193C VAL* 3.0 55.1 - - + +
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Residues in contact with SER1191 (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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1187C ASP 3.0 15.6 + - - -
1188C TYR* 2.7 29.0 + - - -
1190C TRP* 1.3 77.3 - - - +
1192C LEU* 1.3 65.2 + - - +
1193C VAL 3.5 1.7 - - - -
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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
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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