Contacts of the helix formed by residues 1090 - 1097 (chain G) in PDB entry 2F8N
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 ASP1090 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1065G LEU* 4.1 13.0 - - + +
1086G ALA 3.4 19.6 + - - +
1087G VAL 3.0 6.4 + - - +
1088G ALA 5.0 0.2 - - - -
1089G ASN* 1.3 78.5 - - - +
1091G GLU* 1.3 60.7 + - - +
1092G GLU* 3.8 6.2 + - - +
1093G LEU* 3.0 44.4 + - + +
1094G ASN* 2.9 31.3 + - - +
1503H LEU* 5.2 0.3 - - - +
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Residues in contact with GLU1091 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735E ALA 3.4 22.8 - - - +
1089G ASN 3.8 3.6 + - - -
1090G ASP* 1.3 75.8 + - - +
1092G GLU* 1.3 64.7 + - + +
1094G ASN* 3.8 4.9 + - - +
1095G GLN* 3.0 30.3 + - + +
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Residues in contact with GLU1092 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090G ASP* 3.6 6.6 + - - +
1091G GLU* 1.3 84.0 - - + +
1093G LEU* 1.3 57.5 + - - +
1095G GLN* 4.1 1.6 - - - -
1096G LEU* 2.9 23.2 + - - +
1500H PRO* 3.2 29.1 - - + +
1501H GLY* 3.5 8.5 + - - -
1502H GLU* 2.6 41.6 + - - +
1503H LEU* 2.8 37.8 + - + +
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Residues in contact with LEU1093 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058G LEU* 5.3 3.1 - - + +
1061G GLU* 4.6 16.2 - - + +
1062G ILE* 3.8 36.1 - - + -
1065G LEU* 3.9 18.8 - - + -
1086G ALA 4.3 5.2 - - - +
1087G VAL* 4.0 15.0 - - + -
1090G ASP* 3.0 36.6 + - + +
1092G GLU* 1.3 72.3 - - - +
1094G ASN* 1.3 61.6 + - - +
1095G GLN 3.0 1.6 - - - -
1096G LEU* 3.0 16.4 + - + +
1097G LEU* 2.8 35.8 + - + +
1462H PHE* 5.5 1.1 - - + -
1503H LEU* 3.9 19.5 - - + -
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Residues in contact with ASN1094 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087G VAL* 3.3 17.0 + - - +
1088G ALA* 3.8 26.9 + - - +
1090G ASP 2.9 20.9 + - - +
1091G GLU* 3.8 4.9 + - - +
1093G LEU* 1.3 77.2 - - - +
1095G GLN* 1.3 61.0 + - - +
1097G LEU* 3.8 2.6 - - - +
1098G LYS* 3.4 25.6 + - - +
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Residues in contact with GLN1095 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734E ARG 5.0 1.0 - - - +
735E ALA* 3.8 28.9 - - - +
1091G GLU* 3.0 18.3 + - + +
1092G GLU* 3.4 7.9 - - - +
1093G LEU 3.0 0.4 - - - -
1094G ASN* 1.3 74.9 - - - +
1096G LEU* 1.3 63.4 + - - +
1097G LEU 3.0 5.1 + - - -
1098G LYS* 3.2 48.8 + - - +
1500H PRO* 3.9 17.0 - - + -
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Residues in contact with LEU1096 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058G LEU* 4.3 16.4 - - + -
1092G GLU 2.9 17.4 + - - +
1093G LEU* 3.0 11.6 + - + +
1095G GLN* 1.3 77.4 - - - +
1097G LEU* 1.3 64.6 + - + +
1098G LYS 3.6 1.1 + - - +
1462H PHE* 4.4 15.5 - - + -
1466H VAL* 5.1 5.2 - - + -
1469H ARG* 2.9 48.0 + - - +
1498H LEU* 3.8 11.4 - - + +
1499H LEU* 3.3 35.2 - - + -
1500H PRO* 4.2 8.1 - - + -
1503H LEU* 4.2 16.8 - - + -
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Residues in contact with LEU1097 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TYR* 3.5 30.3 - - + +
1062G ILE* 4.5 6.5 - - + -
1087G VAL* 3.7 36.1 - - + -
1093G LEU* 2.8 17.9 + - + +
1094G ASN* 3.6 4.9 + - - +
1095G GLN 3.0 0.2 - - - -
1096G LEU* 1.3 91.5 - - + +
1098G LYS* 1.3 64.7 + - - +
1100G VAL* 3.1 37.2 + - + +
1102G ILE* 5.8 3.4 - - + -
1462H PHE* 4.2 26.9 - - + -
1466H VAL* 5.8 0.2 - - + -
1469H ARG* 3.9 4.9 - - - +
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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