Contacts of the helix formed by residues 1116 - 1126 (chain F) in PDB entry 6C3P
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 PRO1116 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824F GLU 3.3 22.9 - - - +
825F ARG* 3.8 19.1 - - - +
826F GLY 4.5 7.4 - - - +
1114F THR 3.7 6.1 - - - +
1115F THR* 1.3 103.8 - - + +
1117F LEU* 1.3 66.4 + - - +
1118F GLY 3.3 2.1 + - - +
1119F SER* 3.4 20.5 + - - +
1120F ILE* 3.7 1.9 + - - +
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Residues in contact with LEU1117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503F LEU* 3.5 40.2 - - + +
504F ARG* 4.4 28.9 - - - +
506F ILE* 5.2 2.7 - - + -
824F GLU 4.5 2.6 + - - -
1112F PHE* 4.7 25.8 - - + +
1115F THR 3.7 2.2 + - - +
1116F PRO* 1.3 71.3 - - - +
1118F GLY* 1.3 67.8 + - - +
1120F ILE* 3.3 13.8 - - + +
1121F LEU* 2.9 29.0 + - + +
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Residues in contact with GLY1118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824F GLU* 4.8 7.4 + - - +
1116F PRO* 3.3 2.8 - - - +
1117F LEU* 1.3 79.8 - - - +
1119F SER* 1.3 61.6 + - - +
1121F LEU* 3.6 10.9 - - - +
1122F ASN* 2.9 25.1 + - - +
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Residues in contact with SER1119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115F THR* 4.9 5.8 - - - -
1116F PRO* 3.4 20.9 + - - +
1117F LEU 3.2 0.8 - - - -
1118F GLY* 1.3 73.8 - - - +
1120F ILE* 1.3 57.5 + - - +
1122F ASN* 2.8 29.5 + - - +
1123F ARG* 3.0 31.7 - - - +
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Residues in contact with ILE1120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503F LEU* 4.7 9.9 - - + -
1100F LEU* 6.0 0.7 - - + -
1104F ILE* 3.7 42.0 - - + -
1111F PHE* 3.9 26.9 - - + -
1112F PHE* 5.8 4.0 - - + -
1115F THR* 4.3 14.3 - - + +
1116F PRO 3.7 8.7 + - - +
1117F LEU* 3.3 25.4 - - + +
1119F SER* 1.3 77.5 - - - +
1121F LEU* 1.3 62.8 + - - +
1123F ARG* 3.8 11.5 + - + +
1124F PHE* 3.7 17.8 - - + -
1317F LEU* 4.2 22.7 - - + -
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Residues in contact with LEU1121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499F THR* 3.9 30.5 - - + +
500F ASN* 3.1 34.3 - - - +
503F LEU* 4.9 9.9 - - + -
504F ARG* 3.9 25.1 - - - +
1117F LEU* 2.9 20.7 + - + +
1118F GLY* 3.6 10.3 - - - +
1120F ILE* 1.3 74.7 - - + +
1122F ASN* 1.3 64.5 + - - +
1123F ARG 3.1 3.8 + - - -
1124F PHE* 3.1 7.3 + - - +
1125F SER* 2.9 25.8 + - - -
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Residues in contact with ASN1122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118F GLY 2.9 13.1 + - - +
1119F SER* 2.8 16.4 + - - +
1121F LEU* 1.3 73.0 - - - +
1123F ARG* 1.3 71.7 + - - +
1125F SER* 3.5 9.1 + - - -
1126F SER* 2.8 42.7 + - - -
1127F ASP* 3.1 10.3 + - - +
1197F LEU* 5.2 12.5 - - - +
1200F LEU* 5.2 10.8 - - - +
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Residues in contact with ARG1123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100F LEU* 4.5 11.3 - - + +
1119F SER* 3.0 44.9 + - - +
1120F ILE* 4.0 10.1 - - + +
1121F LEU 3.1 1.2 - - - -
1122F ASN* 1.3 93.3 - - - +
1124F PHE* 1.3 58.7 + - + +
1127F ASP* 3.2 32.2 + - - +
1128F CYS* 2.9 26.9 + - - +
1313F ARG* 3.3 29.8 - - + +
1314F ILE* 3.6 21.2 - - + +
1317F LEU* 3.2 35.1 - - + +
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Residues in contact with PHE1124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495F ARG* 2.8 35.0 + - - +
499F THR* 4.6 19.5 - - + +
503F LEU* 5.4 5.4 - - + -
1097F HIS* 4.1 25.1 - + - -
1100F LEU* 3.5 33.2 - - + -
1101F LEU* 3.6 46.7 - - + -
1104F ILE* 3.8 25.6 - - + -
1120F ILE* 3.7 19.7 - - + -
1121F LEU* 3.1 8.2 + - - +
1123F ARG* 1.3 79.5 - - + +
1125F SER* 1.3 64.0 + - - +
1126F SER 3.6 0.2 - - - -
1128F CYS* 3.7 13.0 - - + +
1129F ASN 4.4 0.3 + - - -
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Residues in contact with SER1125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419F ASN* 5.2 7.3 + - - -
423F ILE* 6.0 0.5 - - - +
492F SER* 5.7 0.3 + - - -
495F ARG* 4.2 1.7 + - - -
496F LEU* 3.5 33.4 - - - +
500F ASN* 5.7 0.9 - - - -
1121F LEU* 2.9 25.8 + - - +
1122F ASN* 3.1 12.6 + - - -
1124F PHE* 1.3 81.3 - - - +
1126F SER* 1.3 61.9 + - - +
1129F ASN* 3.6 16.5 + - - +
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Residues in contact with SER1126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F ILE* 4.3 20.7 - - - +
1122F ASN* 2.8 25.6 + - - -
1125F SER* 1.3 76.2 - - - +
1127F ASP* 1.3 64.6 + - - +
1128F CYS 3.5 1.3 - - - -
1129F ASN* 3.4 8.4 + - - +
1130F THR* 2.8 38.0 + - - -
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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