Contacts of the helix formed by residues 629 - 640 (chain B) in PDB entry 2O8C
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 ASP 629 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543B LYS* 5.8 2.0 - - - +
597B GLU* 6.0 0.2 - - - -
624B GLY* 4.6 10.7 + - - -
627B PHE 3.8 1.6 + - - -
628B TRP* 1.3 73.9 - - - +
630B ALA* 1.3 61.0 + - - +
631B SER* 3.5 11.7 + - - +
632B LYS* 2.9 30.6 + - - +
633B THR* 2.8 23.2 + - - -
635B ARG* 4.7 2.8 + - - -
682B SER* 3.6 8.5 - - - -
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Residues in contact with ALA 630 (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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629B ASP* 1.3 75.1 - - - +
631B SER* 1.3 61.8 + - - +
633B THR* 3.1 13.7 + - - -
634B LEU* 3.3 13.9 + - - +
673B PRO* 3.6 29.0 - - + +
678B GLU* 3.4 28.7 - - + +
681B LEU* 3.7 14.0 - - + +
682B SER* 3.6 13.8 - - - +
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Residues in contact with SER 631 (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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629B ASP* 3.3 11.3 - - - +
630B ALA* 1.3 78.1 - - - +
632B LYS* 1.3 59.4 + - - +
634B LEU* 4.1 3.6 + - - +
635B ARG* 3.4 40.1 + - - +
671B LEU 5.5 2.0 - - - +
673B PRO* 3.9 18.6 - - - +
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Residues in contact with LYS 632 (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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624B GLY 3.7 10.2 + - - +
625B SER* 3.4 13.7 + - - +
628B TRP* 3.1 48.2 - - + +
629B ASP* 2.9 21.6 + - - +
631B SER* 1.3 75.4 - - - +
633B THR* 1.3 59.7 + - - +
634B LEU 3.3 0.7 - - - -
635B ARG* 3.3 27.3 + - + +
636B THR* 2.8 40.5 + - - +
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Residues in contact with THR 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B TRP* 3.8 11.6 - - + +
629B ASP 2.8 16.1 + - - -
630B ALA 3.1 7.3 + - - -
632B LYS* 1.3 78.1 - - - +
634B LEU* 1.3 62.0 + - - +
636B THR* 3.4 1.6 + - - -
637B LEU* 3.1 37.3 + - + +
681B LEU* 3.2 31.5 + - + +
684B LEU* 3.9 21.1 - - + -
685B GLY* 3.2 27.6 - - - +
688B VAL* 5.1 1.6 - - + -
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Residues in contact with LEU 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B ALA 3.3 11.2 + - - +
631B SER 4.5 3.6 - - - +
632B LYS 3.3 0.2 - - - -
633B THR* 1.3 75.3 - - - +
635B ARG* 1.3 66.7 + - + +
636B THR 3.4 0.3 + - - -
637B LEU* 3.5 13.5 + - + +
638B LEU* 3.4 28.1 + - - +
655B LEU* 4.5 14.0 - - + +
659B LEU* 5.4 2.0 - - + +
663B THR* 3.9 26.7 - - + -
671B LEU* 3.6 35.7 - - + +
672B THR 3.8 3.6 - - - -
673B PRO* 3.6 29.2 - - + -
681B LEU* 4.1 24.9 - - + -
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Residues in contact with ARG 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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629B ASP* 4.7 3.2 + - - -
631B SER* 3.4 32.0 + - - +
632B LYS* 3.3 37.3 + - + +
633B THR 3.3 0.4 - - - -
634B LEU* 1.3 79.5 - - - +
636B THR* 1.3 62.0 + - - +
638B LEU* 3.5 6.4 + - - +
639B GLU* 3.1 42.6 + - - +
671B LEU 6.1 1.1 - - - +
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Residues in contact with THR 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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628B TRP* 3.7 37.6 - - + -
632B LYS* 2.8 28.0 + - - +
633B THR 3.8 4.3 - - - -
634B LEU 3.3 0.2 - - - -
635B ARG* 1.3 76.3 - - - +
637B LEU* 1.3 60.2 + - - +
638B LEU 3.0 0.7 + - - -
639B GLU* 3.1 9.5 + - - -
640B GLU* 2.9 50.2 + - + +
642B TYR* 4.6 6.1 - - + +
688B VAL* 4.9 2.2 - - + -
692B LYS* 5.0 3.1 - - - -
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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
----------------------------------------------------------
628B TRP* 6.4 0.2 - - + -
633B THR* 3.1 26.4 + - + +
634B LEU* 3.9 13.7 - - + +
635B ARG 3.4 0.2 - - - -
636B THR* 1.3 76.6 - - - +
638B LEU* 1.3 62.4 + - - +
641B GLU* 4.0 0.7 + - - -
642B TYR* 3.7 45.9 + - + -
643B PHE* 4.1 25.3 - - + -
655B LEU* 4.4 13.0 - - + -
659B LEU* 4.1 18.2 - - + -
684B LEU* 3.9 25.1 - - + -
688B VAL* 4.2 25.1 - - + -
701B LEU* 4.6 4.9 - - + -
706B PHE* 5.8 0.4 - - + -
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Residues in contact with LEU 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 LEU* 3.4 17.2 + - + +
635B ARG* 3.9 7.0 - - - +
636B THR 3.1 0.6 - - - -
637B LEU* 1.3 77.4 - - + +
639B GLU* 1.3 66.8 + - + +
640B GLU 3.3 0.2 - - - -
641B GLU* 3.1 28.5 + - - +
643B PHE* 5.6 2.5 - - + -
653B VAL* 4.8 23.7 - - + +
654B MET 6.0 0.2 - - - -
655B LEU* 4.3 25.6 - - + +
671B LEU* 3.7 32.3 - - + -
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Residues in contact with GLU 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B ARG* 3.1 33.5 + - - +
636B THR* 3.1 7.3 + - - +
638B LEU* 1.3 79.8 - - + +
640B GLU* 1.3 67.0 + - + +
641B GLU* 3.2 12.4 + - - +
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Residues in contact with GLU 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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636B THR* 2.9 27.9 + - + +
639B GLU* 1.3 81.3 - - + +
641B GLU* 1.3 68.9 + - - +
642B TYR* 3.3 42.1 + - + +
692B LYS* 3.6 25.0 + - - -
697B ASP* 5.3 0.9 - - - +
698B GLN* 4.9 12.0 + - - +
832B LEU* 3.8 17.8 - - - +
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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