Contacts of the helix formed by residues 1028 - 1033 (chain C) in PDB entry 3KBU
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 TYR1028 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025C GLY 3.1 23.0 + - - +
1027C SER* 1.3 87.5 - - - +
1029C LEU* 1.3 53.3 + - - +
1030C ASP 3.4 0.7 - - - -
1031C GLN* 3.3 36.3 + - + +
1032C ILE* 2.8 46.9 + - + +
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Residues in contact with LEU1029 (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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990C ILE* 4.1 12.6 - - + -
1025C GLY 4.0 1.9 + - - +
1026C GLU* 3.1 30.5 - - + +
1027C SER 3.2 1.8 - - - -
1028C TYR* 1.3 75.1 - - - +
1030C ASP* 1.3 60.5 + - - +
1032C ILE* 3.1 8.8 + - + +
1033C LEU* 2.8 37.0 + - - +
1040C LEU* 3.7 28.9 - - + -
1041C GLY 5.8 0.7 - - - +
1053C ARG* 3.7 42.2 - - - +
1055C ILE* 4.3 14.4 - - + -
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Residues in contact with ASP1030 (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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1027C SER 4.3 8.1 + - - +
1028C TYR 3.4 0.6 - - - -
1029C LEU* 1.3 78.3 - - - +
1031C GLN* 1.3 62.5 + - - +
1033C LEU* 3.4 24.2 + - - +
1034C ASN* 3.7 3.8 + - - -
1035C GLY 4.5 3.8 + - - -
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Residues in contact with GLN1031 (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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1027C SER 5.2 0.4 + - - +
1028C TYR* 3.3 39.8 + - + +
1030C ASP* 1.3 75.2 - - - +
1032C ILE* 1.3 68.9 + - + +
1034C ASN* 3.0 19.4 + - - +
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Residues in contact with ILE1032 (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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939C PRO* 3.5 17.1 - - + +
987C SER* 4.2 13.1 + - - -
988C PRO* 3.6 36.8 - - + +
990C ILE* 4.0 25.4 - - + -
1025C GLY 5.1 3.1 - - - +
1028C TYR* 2.8 37.7 + - + +
1029C LEU* 3.1 10.5 + - + +
1031C GLN* 1.3 74.3 - - + +
1033C LEU* 1.3 60.1 + - - +
1034C ASN* 3.0 9.0 + - - +
1055C ILE* 3.7 37.0 - - + -
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Residues in contact with LEU1033 (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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937C VAL* 4.5 17.0 - - + -
939C PRO* 4.1 5.8 - - + -
940C PRO* 3.6 3.8 - - - +
990C ILE* 4.0 24.7 - - + -
1029C LEU 2.8 21.6 + - - +
1030C ASP* 3.4 16.8 - - - +
1031C GLN 3.2 0.4 - - - -
1032C ILE* 1.3 76.2 - - + +
1034C ASN* 1.3 65.1 + - - +
1035C GLY 2.9 3.2 + - - +
1036C MET* 3.0 43.3 + - - +
1038C GLU* 4.0 22.2 - - + +
1040C LEU* 4.0 22.2 - - + -
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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