Contacts of the helix formed by residues 633 - 644 (chain B) in PDB entry 3KN5
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 SER 633 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632B THR* 1.3 81.0 + - - +
634B ALA* 1.3 64.9 + - - +
635B VAL* 3.8 5.7 + - - +
636B GLU* 3.1 28.6 + - - +
637B ILE* 3.0 24.9 + - - +
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Residues in contact with ALA 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632B THR 4.1 0.2 + - - -
633B SER* 1.3 73.0 - - - +
635B VAL* 1.3 55.5 + - + +
637B ILE* 3.4 5.8 + - - +
638B MET* 2.8 49.2 + - + +
717B ALA* 5.6 1.8 - - - +
720B HIS* 4.4 25.4 - - + +
721B ALA* 3.8 9.4 - - + +
724B LYS* 5.0 4.9 - - + -
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Residues in contact with VAL 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633B SER* 3.3 6.3 + - - +
634B ALA* 1.3 76.3 - - + +
636B GLU* 1.3 70.4 + - - +
638B MET* 3.8 16.6 - - + +
639B LYS* 3.3 40.2 + - - +
724B LYS* 6.0 3.6 - - - -
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Residues in contact with GLU 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632B THR* 2.9 29.6 - - + +
633B SER* 3.1 24.5 + - - +
635B VAL* 1.3 81.8 - - - +
637B ILE* 1.3 63.8 + - - +
639B LYS* 3.2 28.4 + - - +
640B LYS* 3.4 29.7 + - - +
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Residues in contact with ILE 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B PHE* 4.1 23.8 - - + +
623B GLN* 3.4 19.7 - - - +
631B CYS* 4.4 0.7 - - - -
632B THR* 3.2 32.5 - - + +
633B SER 3.0 12.7 + - - +
634B ALA* 3.8 6.5 - - - +
636B GLU* 1.3 74.1 - - - +
638B MET* 1.3 63.4 + - - +
639B LYS 3.1 0.7 + - - -
640B LYS* 3.1 4.3 + - - +
641B ILE* 3.0 33.0 + - + +
717B ALA* 4.1 30.3 - - + +
718B THR* 4.1 12.6 - - + +
721B ALA* 3.8 14.6 - - + -
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Residues in contact with MET 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634B ALA* 2.8 34.6 + - + +
635B VAL* 3.8 16.2 - - + +
636B GLU 3.3 0.2 - - - -
637B ILE* 1.3 72.6 - - - +
639B LYS* 1.3 60.1 + - - +
641B ILE* 3.6 7.5 + - - +
642B LYS* 3.3 34.9 + - - +
721B ALA* 3.9 10.7 - - + +
724B LYS* 3.2 40.6 - - + +
725B TYR* 3.6 35.4 - - + +
728B GLU* 4.2 12.6 - - - +
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Residues in contact with LYS 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635B VAL* 3.3 33.9 + - - +
636B GLU* 3.2 24.0 + - - +
637B ILE 3.1 0.6 - - - -
638B MET* 1.3 78.0 - - - +
640B LYS* 1.3 66.0 + - + +
641B ILE 3.2 0.2 - - - -
642B LYS* 3.3 21.8 - - + +
643B LYS* 3.2 26.9 + - + +
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Residues in contact with LYS 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B PHE* 3.5 29.8 + - + +
623B GLN 3.7 21.5 + - - +
624B SER* 4.6 3.8 - - - +
625B HIS* 4.5 14.1 - - + +
632B THR* 5.2 1.2 - - - +
636B GLU* 3.4 30.4 + - - +
637B ILE 3.1 6.8 + - - +
639B LYS* 1.3 78.7 - - + +
641B ILE* 1.3 56.6 + - - +
643B LYS* 3.2 1.7 + - - -
644B GLY 2.8 10.0 + - - -
645B ASP* 2.8 67.8 + - + +
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Residues in contact with ILE 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B TRP* 3.8 28.6 + - + +
622B PHE* 3.7 27.1 - - + -
637B ILE* 3.0 32.0 + - + +
638B MET* 3.7 8.7 - - - +
639B LYS 3.2 0.2 - - - -
640B LYS* 1.3 75.4 - - - +
642B LYS* 1.3 63.7 + - - +
643B LYS 3.2 0.2 + - - -
644B GLY* 3.2 2.1 + - - -
668B LEU 5.1 0.2 - - - +
670B VAL* 3.0 23.1 - - + +
718B THR* 4.1 3.6 - - + +
721B ALA* 4.4 2.9 - - + -
722B PHE* 3.9 37.2 - - + +
725B TYR* 4.0 25.7 - - + -
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Residues in contact with LYS 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B MET* 3.3 24.4 + - - +
639B LYS* 3.3 27.3 - - + +
641B ILE* 1.3 79.5 - - - +
643B LYS* 1.3 57.3 + - + +
670B VAL* 3.6 18.4 - - - +
725B TYR* 3.6 39.3 + - + +
728B GLU 5.5 3.9 + - - -
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Residues in contact with LYS 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639B LYS* 3.2 19.1 + - + +
640B LYS* 3.8 3.4 - - - +
641B ILE 3.1 0.6 - - - -
642B LYS* 1.3 78.4 - - + +
644B GLY* 1.3 65.0 + - - +
645B ASP* 4.2 19.6 + - + +
670B VAL 4.1 7.5 - - - +
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Residues in contact with GLY 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B PHE* 4.6 1.3 - - - -
640B LYS 2.8 6.7 + - - -
641B ILE 3.2 5.9 + - - -
643B LYS* 1.3 79.2 - - - +
645B ASP* 1.3 56.7 + - - -
646B PHE* 3.4 31.8 + - - +
668B LEU 4.3 1.3 - - - -
669B THR* 5.1 0.2 - - - -
670B VAL* 3.3 25.3 - - - +
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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