Contacts of the strand formed by residues 200 - 203 (chain 1) 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 CYS 200 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1261 LEU* 3.2 32.1 - - + -
1611 PHE* 3.9 15.0 - - + -
1641 ILE 3.9 3.1 - - - -
1651 THR* 4.0 6.1 - - - -
1991 ASN* 1.3 81.1 - - - +
2011 VAL* 1.3 66.4 + - - +
2111 ASP* 3.1 8.5 - - - +
2121 VAL* 2.8 32.4 + - - +
2141 CYS* 2.0 51.8 - - - -
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Residues in contact with VAL 201 (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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1611 PHE* 3.5 7.4 - - - -
1621 LEU* 2.9 40.5 + - + +
1641 ILE* 3.5 30.1 + - + +
1731 PHE* 3.8 17.0 - - + -
1861 TRP* 3.7 25.8 - - + -
2001 CYS* 1.3 83.6 - - - +
2021 VAL* 1.3 75.2 + - - +
2091 TRP* 3.9 24.0 - - + -
2101 ASN 3.5 8.1 - - - +
2121 VAL 4.6 0.2 - - - +
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Residues in contact with VAL 202 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1591 VAL* 3.5 22.0 - - + -
1601 ALA 3.2 10.5 - - - +
1611 PHE* 3.7 17.3 - - + -
1621 LEU* 4.5 1.3 - - - -
2011 VAL* 1.3 79.3 - - - +
2031 LEU* 1.3 59.2 + - - +
2041 LEU* 4.3 4.9 - - + -
2091 TRP* 3.3 7.1 - - - +
2101 ASN* 2.9 50.8 + - + +
2121 VAL* 3.6 33.9 - - + -
2181 PHE* 3.7 21.8 - - + -
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Residues in contact with LEU 203 (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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1491 ASN* 3.7 14.4 - - - +
1521 ILE* 3.8 16.6 - - + +
1531 GLN* 3.4 41.1 - - + +
1561 ALA* 5.0 6.7 - - + -
1581 ASP 4.4 1.2 - - - +
1591 VAL* 3.4 5.9 - - - -
1601 ALA* 2.7 34.4 + - + +
1621 LEU* 4.1 17.1 - - + +
2021 VAL* 1.3 70.8 - - - +
2041 LEU* 1.3 67.6 + - - +
2071 GLY* 2.9 34.8 - - - +
2081 LYS 3.7 1.6 - - - -
2091 TRP* 3.7 13.7 - - + +
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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