Contacts of the strand formed by residues 160 - 165 (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 ALA 160 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561 ALA* 4.2 5.4 - - + -
1581 ASP 3.2 7.1 + - - +
1591 VAL* 1.3 76.4 - - - +
1611 PHE* 1.3 63.5 + - - +
1621 LEU* 6.4 0.2 - - + -
2021 VAL* 3.2 5.5 - - - -
2031 LEU* 2.7 42.4 + - + +
2181 PHE* 4.3 0.7 - - - -
2191 LEU* 3.2 25.4 - - + +
2201 VAL* 4.1 0.4 - - - +
2211 VAL* 3.9 27.4 - - + -
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Residues in contact with PHE 161 (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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1241 MET 3.2 27.1 - - - -
1261 LEU* 3.4 42.0 - - + -
1291 ALA* 4.3 6.7 - - + -
1401 VAL* 3.6 14.3 - - + +
1601 ALA* 1.3 75.6 - - - +
1621 LEU* 1.3 64.6 + - - +
2001 CYS* 3.9 23.1 - - + -
2011 VAL 3.5 15.3 - - - -
2021 VAL* 3.7 4.9 - - + +
2121 VAL* 3.9 9.0 - - + -
2131 PRO 4.4 1.6 - - - -
2141 CYS 4.1 5.6 - - - -
2161 ASP 3.3 20.4 - - - -
2181 PHE* 3.5 22.6 - + + +
2191 LEU 2.9 21.8 + - - +
2201 VAL* 4.6 4.9 - - + -
2211 VAL* 3.8 15.2 + - - +
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Residues in contact with LEU 162 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261 LEU* 4.3 8.7 - - - +
1401 VAL* 3.4 7.9 - - - +
1411 ALA* 3.2 15.3 - - + +
1431 PRO* 3.8 19.3 - - + -
1521 ILE* 4.1 23.3 - - + -
1601 ALA 4.8 0.2 - - - +
1611 PHE* 1.3 82.3 - - - +
1631 GLY* 1.3 58.2 + - - +
1641 ILE* 2.9 24.5 + - + +
2011 VAL* 2.9 26.2 + - + +
2031 LEU* 4.1 23.6 - - + +
2091 TRP* 3.7 45.1 - - + +
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Residues in contact with GLY 163 (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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1401 VAL* 3.4 21.5 - - - +
1411 ALA 2.7 14.8 + - - -
1421 THR* 3.1 19.7 + - - -
1621 LEU* 1.3 68.0 - - - +
1641 ILE* 1.3 60.7 - - - +
1751 ASP* 3.1 20.4 - - - -
1761 LEU* 3.3 22.0 + - - -
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Residues in contact with ILE 164 (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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1261 LEU* 5.9 0.2 - - - +
1421 THR* 4.0 18.8 - - + -
1431 PRO* 4.6 2.7 - - + +
1621 LEU* 2.9 21.0 + - + +
1631 GLY* 1.3 82.5 - - - +
1651 THR* 1.3 74.8 + - - +
1731 PHE* 3.8 30.7 - - + -
1741 GLU 3.4 10.5 - - - +
1811 VAL* 4.1 19.1 - - + -
2001 CYS* 4.7 0.2 - - - +
2011 VAL* 3.5 33.0 + - + -
2091 TRP* 3.5 41.1 - - + -
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Residues in contact with THR 165 (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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1261 LEU* 4.1 8.3 - - + -
1641 ILE* 1.3 84.4 - - - +
1661 ASP* 1.3 62.0 + - - +
1671 GLN* 3.5 20.6 + - + +
1681 ARG* 5.1 0.3 + - - +
1721 VAL 3.6 0.5 - - - +
1731 PHE* 3.5 7.1 - - - -
1741 GLU* 3.0 38.6 + - - +
1751 ASP 5.5 0.5 + - - -
1761 LEU* 4.0 22.7 - - + +
1991 ASN 3.1 15.7 - - - +
2001 CYS* 4.0 17.7 - - - +
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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