Contacts of the strand formed by residues 172 - 175 (chain 2) in PDB entry 1KZC
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 VAL 172 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1652 THR 3.7 0.9 - - - +
1662 ASP* 3.3 18.9 - - - +
1682 ARG* 4.0 21.7 + - - +
1692 THR* 3.1 35.4 + - + +
1702 GLU 4.0 2.0 - - - +
1712 ASN* 1.3 81.2 - - - +
1732 PHE* 1.3 59.3 + - - +
1742 GLU* 3.7 15.4 + - + +
1802 ARG* 4.1 41.5 - - - +
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Residues in contact with PHE 173 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1642 ILE* 3.7 20.6 - - + -
1652 THR 3.4 9.9 - - - -
1662 ASP* 3.5 34.8 - - + -
1702 GLU* 5.6 0.2 - - - -
1712 ASN* 3.9 33.4 + - - -
1722 VAL* 1.3 74.0 - - - +
1742 GLU* 1.3 60.5 + - - +
1802 ARG* 3.6 11.1 - - - +
1812 VAL* 3.1 33.1 + - + +
1842 THR* 5.9 0.9 - - + -
1862 TRP* 3.6 41.1 - + + -
1912 PRO* 3.9 13.9 - - + -
1982 GLU 5.4 0.2 - - - -
1992 ASN 4.9 1.6 - - - -
2012 VAL* 3.9 9.9 - - + -
2092 TRP* 6.4 0.2 - - + -
2112 ASP* 4.7 8.3 - - + -
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Residues in contact with GLU 174 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1642 ILE* 3.4 1.9 - - - -
1652 THR* 2.9 34.7 + - - +
1682 ARG* 2.7 54.9 + - - +
1722 VAL* 3.9 14.7 - - + +
1732 PHE* 1.3 79.9 - - - +
1752 ASP* 1.3 69.9 + - - +
1782 GLY* 3.6 25.7 - - - +
1792 ASN 3.2 14.8 - - - +
1802 ARG* 4.2 9.6 + - - +
1812 VAL* 4.0 6.1 - - - +
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Residues in contact with ASP 175 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1422 THR* 4.0 9.6 - - + +
1442 ARG* 2.9 42.3 + - - +
1632 GLY 3.1 13.2 - - - +
1652 THR* 5.6 1.3 + - - -
1742 GLU* 1.3 78.1 - - - +
1762 LEU* 1.3 62.9 + - - +
1772 THR* 2.8 34.2 + - - -
1782 GLY* 3.0 9.9 + - - -
1792 ASN* 2.7 44.7 + - - +
1812 VAL* 3.8 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