Contacts of the helix formed by residues 482 - 488 (chain A) in PDB entry 1K2P
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 LEU 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A GLY 4.0 0.4 + - - -
481A CYS* 1.3 72.0 - - - +
483A LEU* 1.3 56.5 + - - +
485A TYR* 3.4 5.9 - - + +
486A LEU* 2.8 44.3 + - + +
501A MET* 3.7 29.4 - - + -
524A ALA* 3.5 11.6 + - + +
527A CYS* 2.7 31.1 + - + -
529A VAL* 4.0 11.6 - - + +
535A VAL* 3.9 23.1 - - + -
586A LEU* 3.8 29.8 - - + -
590A ILE* 4.2 15.3 - - + -
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A CYS* 3.1 12.2 - - - -
482A LEU* 1.3 80.4 - - - +
484A ASN* 1.3 62.1 + - - +
486A LEU* 3.4 11.4 + - - +
487A ARG* 3.3 57.5 + - - +
524A ALA* 3.4 25.8 + - + +
525A ARG* 4.1 11.0 - - + +
589A GLU* 4.3 9.9 - - - +
594A GLY* 3.8 14.8 - - - +
595A LYS 5.4 0.4 - - - +
433B LYS* 3.4 30.3 - - + +
434B GLU 4.0 16.4 - - - +
435B GLY* 5.0 2.5 - - - +
469B PRO* 6.2 0.2 - - + -
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Residues in contact with ASN 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A ASN 3.9 11.5 + - - -
480A GLY* 5.2 2.0 - - - -
481A CYS* 3.1 22.0 + - - +
483A LEU* 1.3 79.0 - - - +
485A TYR* 1.3 63.5 + - - +
487A ARG* 3.3 6.6 + - - +
488A GLU* 3.0 44.9 + - - +
433B LYS* 5.7 0.2 - - - +
468B ARG* 5.9 0.7 + - - -
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Residues in contact with TYR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A ASN* 3.4 43.3 + - + +
481A CYS 3.0 13.5 + - - +
482A LEU* 3.2 9.8 + - + +
484A ASN* 1.3 79.2 - - - +
486A LEU* 1.3 62.0 + - - +
487A ARG 3.3 0.9 + - - -
488A GLU* 3.6 25.9 + - - +
490A ARG* 3.4 43.2 - - + +
491A HIS 4.4 0.5 + - - -
493A PHE* 3.9 19.1 - + - -
501A MET* 3.9 25.1 - - + -
529A VAL* 3.8 31.0 - - + -
533A GLY* 4.2 13.1 - - - -
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A LEU* 2.8 50.5 + - + +
483A LEU* 3.7 5.8 - - - +
484A ASN 3.3 0.2 - - - -
485A TYR* 1.3 73.0 - - - +
487A ARG* 1.3 51.8 + - - +
491A HIS* 2.5 37.0 + - - -
493A PHE* 3.8 23.8 - - + -
498A LEU* 5.5 0.7 - - + -
501A MET* 3.9 15.0 - - + -
524A ALA* 4.9 6.7 - - + -
589A GLU 3.6 24.0 - - - +
590A ILE* 3.8 17.3 - - + +
593A LEU* 3.6 8.1 - - + +
594A GLY* 3.7 21.5 - - - +
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Residues in contact with ARG 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A LEU* 3.3 39.1 + - - +
484A ASN* 3.3 5.7 + - - +
485A TYR 3.2 0.4 - - - -
486A LEU* 1.3 81.2 - - - +
488A GLU* 1.3 68.6 + - - +
491A HIS* 3.6 19.1 - - + +
593A LEU 4.2 7.6 - - - +
594A GLY* 2.7 30.4 + - - +
595A LYS* 4.5 10.9 - - - +
596A MET 4.4 2.8 - - - +
434B GLU* 2.6 71.8 + - - +
468B ARG* 5.9 0.7 - - - +
469B PRO* 4.3 10.2 - - - +
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Residues in contact with GLU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A ASN* 4.0 7.7 + - - +
484A ASN* 3.0 38.6 + - - +
485A TYR* 3.6 33.7 + - - +
487A ARG* 1.3 84.4 - - - +
489A MET* 1.3 69.3 + - - +
490A ARG* 3.1 34.7 + - - +
491A HIS* 2.8 28.6 + - - +
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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