Contacts of the strand formed by residues 1463 - 1466 (chain D) in PDB entry 1KI1
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 PHE1463 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429D ASN* 2.7 18.0 + - - +
1432D ARG* 3.5 31.2 - - + -
1433D LEU* 3.7 19.5 - - + +
1436D ILE* 4.0 9.0 - - + -
1462D LYS* 1.3 74.1 - - - +
1464D LEU* 1.3 69.7 + - - +
1465D HIS* 3.4 38.8 - - - -
1466D SER* 3.6 18.6 - - - -
1481D PHE* 4.2 13.5 - + + -
1482D LEU 3.8 5.6 - - - -
1483D PHE* 3.8 19.7 - + - -
1504D VAL* 5.5 0.2 - - + -
1505D PHE* 3.7 22.2 - + - -
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Residues in contact with LEU1464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1462D LYS* 4.5 12.3 - - + +
1463D PHE* 1.3 87.1 - - - +
1465D HIS* 1.3 62.5 + - - +
1482D LEU* 2.8 29.5 + - + +
1483D PHE 3.5 29.6 - - - +
1484D ASN* 3.8 8.7 - - + +
1564D LYS* 3.4 22.6 + - + +
1568D ALA* 3.6 26.5 - - + -
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Residues in contact with HIS1465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463D PHE* 3.4 14.1 - - - -
1464D LEU* 1.3 81.8 - - - +
1466D SER* 1.3 97.7 + - - +
1467D GLY* 4.1 2.5 - - - -
1481D PHE* 3.3 1.0 - - - -
1482D LEU* 2.6 44.2 + - + +
1557D GLU* 4.9 11.0 + - + +
1560D ALA* 4.6 14.5 - - + +
1561D TRP* 3.4 38.8 + + + -
1564D LYS* 3.0 39.0 - - + +
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Residues in contact with SER1466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1463D PHE* 3.6 14.1 - - - -
1465D HIS* 1.3 95.5 + - - +
1467D GLY* 1.3 57.8 + - - +
1479D TYR* 3.1 20.0 + - - -
1480D GLY 3.0 22.0 - - - -
1481D PHE* 3.7 19.7 - - - -
1504D VAL* 3.9 13.3 - - - +
1505D PHE* 4.8 0.2 - - - -
1557D GLU* 5.4 0.2 - - - +
1561D TRP* 3.6 2.0 - - - -
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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