Contacts of the helix formed by residues 633 - 644 (chain B) in PDB entry 1HKB
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 VAL 633 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575B PHE* 3.9 7.4 - - + -
600B PHE* 4.2 14.4 - - + -
602B PHE* 3.5 38.1 - - + -
606B CYS* 4.4 2.7 - - - -
614B GLY* 2.8 24.7 + - - +
616B LEU* 4.1 19.7 - - + +
631B HIS 4.6 0.7 - - - +
632B ASP* 1.3 69.8 - - - +
634B VAL* 1.3 67.0 + - + +
636B LEU* 3.6 18.0 - - + +
637B LEU* 3.1 22.9 + - - +
654B VAL* 4.0 26.5 - - + -
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Residues in contact with VAL 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B PHE* 5.3 3.6 - - + -
612B ASP* 3.1 31.4 - - - +
613B ALA 4.1 1.3 - - - +
614B GLY 4.2 4.7 - - - +
632B ASP* 2.7 19.3 + - - +
633B VAL* 1.3 70.5 - - + +
635B THR* 1.3 53.6 + - - +
637B LEU* 3.1 7.9 + - - +
638B ARG* 2.6 70.6 + - - +
651B VAL* 3.6 27.8 - - + +
654B VAL* 4.2 18.2 - - + -
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Residues in contact with THR 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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632B ASP* 3.2 29.2 + - - +
634B VAL* 1.3 75.3 - - - +
636B LEU* 1.3 69.7 + - + +
638B ARG* 2.7 30.9 + - + +
639B ASP* 2.7 33.7 + - - +
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Residues in contact with LEU 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B GLY 5.7 3.1 - - - +
575B PHE* 3.6 42.8 - - + +
627B ASP 4.4 6.1 - - - +
628B CYS* 4.0 22.4 - - + +
631B HIS* 3.9 38.4 - - + -
632B ASP 2.8 19.0 + - - +
633B VAL* 3.6 16.4 - - + +
635B THR* 1.3 74.4 - - + +
637B LEU* 1.3 59.4 + - - +
639B ASP* 3.8 10.7 + - - +
640B ALA* 3.4 19.2 + - - +
643B ARG* 4.1 2.9 + - - -
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Residues in contact with LEU 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B LEU* 4.7 6.3 - - + -
575B PHE* 3.8 16.6 - - + -
578B ILE* 4.3 12.1 - - + -
579B VAL* 4.0 20.9 - - + -
582B ILE* 4.2 15.5 - - + -
598B LEU* 4.5 13.7 - - + -
600B PHE* 4.4 19.7 - - + -
633B VAL 3.1 18.3 + - - +
634B VAL* 3.4 3.6 - - - +
635B THR 3.0 0.6 - - - -
636B LEU* 1.3 74.5 - - - +
638B ARG* 1.3 68.6 + - - +
639B ASP 3.1 0.2 - - - -
640B ALA* 3.3 2.9 + - - +
641B ILE* 3.0 31.6 + - + +
651B VAL* 3.9 27.1 - - + -
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Residues in contact with ARG 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ASP* 4.0 21.0 + - - -
632B ASP* 5.4 1.4 + - - -
634B VAL* 2.6 43.8 + - + +
635B THR* 2.7 21.9 + - + +
637B LEU* 1.3 71.6 - - - +
639B ASP* 1.3 64.2 + - - +
641B ILE* 3.2 13.4 + - + +
642B LYS* 3.0 23.3 + - - +
651B VAL* 3.5 35.4 + - + +
912B ARG* 4.8 10.3 - - - +
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Residues in contact with ASP 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 THR* 2.7 38.4 + - - +
636B LEU* 3.9 10.8 - - - +
638B ARG* 1.3 70.6 - - - +
640B ALA* 1.3 67.4 + - - +
641B ILE 2.9 1.6 - - - -
642B LYS* 2.8 23.7 + - - +
643B ARG* 2.8 27.2 + - + +
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Residues in contact with ALA 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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575B PHE* 3.4 30.7 - - + +
576B ASP* 4.1 6.0 - - - +
579B VAL* 3.4 12.7 - - + +
636B LEU 3.4 8.3 + - - +
637B LEU 3.3 7.0 + - - +
639B ASP* 1.3 78.7 - - - +
641B ILE* 1.3 61.4 + - - +
643B ARG* 2.9 32.6 + - - +
644B ARG* 3.3 21.5 + - - +
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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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579B VAL* 4.1 25.6 - - + -
582B ILE* 5.3 0.9 - - + -
637B LEU* 3.0 31.3 + - + +
638B ARG* 3.3 13.5 - - - +
639B ASP 2.9 0.6 - - - -
640B ALA* 1.3 75.2 - - - +
642B LYS* 1.3 67.2 + - + +
644B ARG* 3.4 4.0 + - - +
645B GLU* 3.2 19.1 + - - -
646B GLU 4.7 0.5 + - - -
647B PHE* 4.0 26.0 - - + +
648B ASP* 4.8 9.6 - - - +
649B LEU* 3.5 44.4 - - + +
651B VAL* 5.1 3.8 - - + -
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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 ARG 3.0 12.8 + - - +
639B ASP* 2.8 18.5 + - - +
641B ILE* 1.3 74.1 - - - +
643B ARG* 1.3 56.9 + - + +
645B GLU* 2.9 29.3 - - - +
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Residues in contact with ARG 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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572B GLU* 3.5 39.0 + - - +
575B PHE* 4.7 3.2 - - - +
576B ASP* 3.4 30.9 + - - +
636B LEU 4.1 6.3 + - - -
639B ASP* 2.8 15.3 + - + +
640B ALA* 2.9 46.8 - - - +
642B LYS* 1.3 78.1 - - + +
644B ARG* 1.3 63.4 + - - +
645B GLU* 3.4 12.1 - - - +
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Residues in contact with ARG 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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576B ASP 5.4 1.2 + - - -
579B VAL* 4.1 13.2 - - + -
580B SER* 4.1 24.9 + - - +
583B SER* 4.0 11.8 + - - -
640B ALA 3.3 10.8 + - - +
641B ILE 3.4 7.4 + - - +
643B ARG* 1.3 79.5 - - - +
645B GLU* 1.3 72.3 + - - +
646B GLU* 3.3 47.2 + - + +
647B PHE* 3.8 15.0 - - + -
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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
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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