Contacts of the helix formed by residues 1114 - 1123 (chain R) in PDB entry 3SN6
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 PHE1114 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102R MET* 3.5 26.7 - - + -
1106R MET* 3.5 23.8 - - - -
1110R GLY 3.5 17.0 - - - -
1111R VAL* 3.1 19.7 - - + +
1112R ALA 2.9 2.6 - - - -
1113R GLY* 1.3 80.9 - - - +
1115R THR* 1.3 63.9 + - - +
1116R ASN* 2.8 5.9 + - - -
1117R SER* 2.9 13.6 + - - -
1118R LEU* 2.9 28.4 + - + +
1132R ASN 6.1 0.4 - - - -
1133R LEU* 4.6 17.5 - - + -
1136R SER* 4.4 16.2 - - - -
1138R TRP* 4.0 26.9 - + + -
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Residues in contact with THR1115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083R LYS* 3.8 17.8 + - + +
1112R ALA 3.6 12.9 + - - -
1113R GLY* 3.4 4.4 + - - -
1114R PHE* 1.3 74.0 - - - +
1116R ASN* 1.3 62.2 + - - +
1118R LEU* 3.6 12.1 - - - +
1119R ARG* 2.9 32.2 + - + +
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Residues in contact with ASN1116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114R PHE 2.8 5.9 + - - +
1115R THR* 1.3 72.8 - - - +
1117R SER* 1.3 59.9 + - - +
1119R ARG* 2.7 49.5 + - - +
1120R MET* 3.0 15.4 + - + +
1132R ASN* 3.6 24.0 - - - +
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Residues in contact with SER1117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114R PHE* 2.9 15.7 + - - -
1116R ASN* 1.3 74.5 - - - +
1118R LEU* 1.3 58.1 + - - +
1120R MET* 2.9 31.2 + - - +
1121R LEU* 2.9 20.3 + - - +
1129R ALA* 4.5 2.8 - - - +
1132R ASN* 3.4 23.4 - - - +
1133R LEU* 3.6 38.5 + - - +
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Residues in contact with LEU1118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083R LYS* 4.6 12.3 - - + +
1084R LEU* 3.5 27.8 - - + -
1087R VAL* 3.4 44.7 - - + +
1099R LEU* 4.7 3.6 - - + -
1102R MET* 6.3 1.8 - - - -
1111R VAL* 3.2 31.0 - - + +
1112R ALA* 4.1 8.3 - - - +
1114R PHE* 2.9 27.2 + - + +
1115R THR* 3.6 13.9 - - - +
1117R SER* 1.3 76.7 - - - +
1119R ARG* 1.3 60.2 + - - +
1121R LEU* 3.4 18.3 + - + +
1122R GLN* 3.6 3.6 + - - +
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Residues in contact with ARG1119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115R THR* 2.9 15.2 + - + +
1116R ASN* 2.7 45.5 + - - +
1118R LEU* 1.3 73.1 - - - +
1120R MET* 1.3 80.0 + - - +
1121R LEU 3.1 1.6 - - - -
1122R GLN* 3.0 42.5 + - - +
1123R GLN* 3.1 36.7 + - + +
1125R ARG* 5.8 2.6 - - - +
1132R ASN* 5.7 0.8 - - - +
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Residues in contact with MET1120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116R ASN* 3.0 8.6 + - + +
1117R SER* 2.9 20.0 + - - +
1119R ARG* 1.3 93.2 - - - +
1121R LEU* 1.3 60.4 + - - +
1122R GLN 3.4 0.2 - - - -
1123R GLN* 3.8 7.9 - - - +
1124R LYS 3.5 1.4 + - - -
1125R ARG* 3.2 61.3 + - + +
1128R GLU* 3.8 9.6 - - - +
1129R ALA* 3.6 33.0 - - + -
1132R ASN* 3.0 48.0 - - + +
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Residues in contact with LEU1121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087R VAL* 3.7 19.5 - - + -
1090R SER* 5.1 1.0 - - - -
1091R LEU* 3.4 23.2 - - + +
1099R LEU* 5.6 3.4 - - + -
1102R MET* 6.4 0.2 - - - -
1117R SER* 2.9 18.1 + - - +
1118R LEU* 3.6 19.5 - - + +
1119R ARG 3.1 0.4 - - - -
1120R MET* 1.3 80.7 - - - +
1122R GLN* 1.3 60.9 + - - +
1123R GLN 3.2 0.7 - - - -
1124R LYS* 3.5 2.6 + - - +
1126R TRP* 3.4 43.8 - - + -
1129R ALA* 4.5 11.2 - - + -
1133R LEU* 5.5 4.9 - - + -
1153R PHE* 3.6 46.7 - - + -
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Residues in contact with GLN1122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086R PRO* 4.0 12.5 - - - +
1087R VAL* 3.5 29.7 + - - +
1090R SER* 4.3 24.7 + - - +
1118R LEU 3.6 8.0 + - - +
1119R ARG* 3.0 39.9 - - - +
1121R LEU* 1.3 76.4 - - - +
1123R GLN* 1.3 61.2 + - + +
1124R LYS* 3.3 17.9 + - - -
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Residues in contact with GLN1123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119R ARG* 3.1 47.5 + - + +
1120R MET* 4.2 8.4 - - - +
1121R LEU 3.2 0.2 - - - -
1122R GLN* 1.3 80.7 - - + +
1124R LYS* 1.3 70.6 + - - +
1125R ARG* 3.2 36.9 + - - +
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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