Contacts of the strand formed by residues 204 - 207 (chain 1) in PDB entry 1KZB
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 TRP 204 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381 PRO* 3.4 26.2 - - + -
1441 ASN* 2.8 22.0 + - - -
1571 LEU* 3.7 14.1 - - + +
1591 ILE* 3.5 26.7 - - + -
1761 VAL* 5.0 2.9 - - + -
1781 TYR* 3.4 33.2 - + - -
1791 THR* 3.5 20.6 - - + -
1801 ASN* 2.8 31.3 + - - +
1811 TRP* 3.7 31.7 - + + -
1821 ASN* 2.8 32.4 + - - +
1851 GLU* 3.8 1.4 - - - +
1961 VAL* 4.0 14.6 - - + -
1971 VAL 3.3 7.0 - - - +
1981 LEU* 3.5 15.2 - - + +
1991 LEU* 4.6 0.7 - - - -
2021 GLY 3.7 1.3 - - - -
2031 LYS* 1.3 82.1 - - - +
2051 ASN* 1.3 61.2 + - - +
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Residues in contact with ASN 205 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811 TRP* 4.0 4.9 - - - -
1851 GLU* 2.8 24.1 - - + +
1961 VAL* 3.5 1.2 - - - -
1971 VAL* 2.9 42.1 + - + +
1991 LEU* 4.2 20.5 - - + +
2041 TRP* 1.3 76.2 - - - +
2061 ASP* 1.3 61.1 + - - +
2071 VAL* 3.4 14.5 - - - +
5021 CA 2.5 24.9 - - - -
15011 MAN 3.0 35.1 + - - -
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Residues in contact with ASP 206 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1681 PHE* 4.5 6.6 - - + -
1811 TRP* 3.8 11.7 - - + -
1851 GLU* 2.8 9.5 - - - +
1861 PRO* 3.4 23.6 - - + +
1871 ASN 3.2 4.8 + - - -
1881 ASN* 2.7 31.5 + - - +
1931 GLU* 2.8 20.0 - - - +
1951 CYS 3.1 12.3 - - - +
1961 VAL* 4.4 0.2 - - - +
2051 ASN* 1.3 74.1 + - - +
2071 VAL* 1.3 59.6 + - - +
5021 CA 2.3 51.3 - - - -
15011 MAN 2.9 6.6 + - - -
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Residues in contact with VAL 207 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1561 PHE* 4.0 9.2 - - + -
1931 GLU* 3.6 7.9 - - - -
1941 ASN 3.3 2.8 + - - -
1951 CYS 2.8 36.3 + - - +
1971 VAL* 3.6 30.1 - - + -
2051 ASN* 3.4 19.5 - - - +
2061 ASP* 1.3 80.8 - - - +
2081 PRO* 1.3 76.7 - - + +
2131 PHE* 3.5 35.2 - - + -
15011 MAN 4.2 5.4 - - - +
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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
------------------------------------------------------------
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