Contacts of the helix formed by residues 639 - 650 (chain B) in PDB entry 2OBF
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 CYS 639 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.9 2.7 - - + +
48A CYS* 2.0 62.1 + - - +
129A HIS* 5.5 5.6 - - + +
132A LEU* 4.7 5.6 - - + -
628B GLN* 5.8 0.7 - - - -
631B CYS* 3.8 0.4 - - - -
637B GLY 3.6 2.4 + - - +
638B GLU* 1.3 87.1 - - - +
640B TRP* 1.3 68.3 + - + +
641B GLN* 3.8 5.2 - - - +
642B ASP* 3.2 38.4 + - - +
643B LYS 3.3 1.9 + - - -
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Residues in contact with TRP 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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125A MET* 4.1 11.3 - - + -
128A GLN* 3.0 31.8 + - - -
624B SER* 3.6 30.3 - - - -
627B SER* 3.7 4.5 - - - -
628B GLN* 3.6 46.7 + - + +
631B CYS* 3.6 12.6 - - - +
638B GLU 3.8 0.2 + - - -
639B CYS* 1.3 73.2 - - + +
641B GLN* 1.3 98.0 + - + +
643B LYS* 3.1 3.5 + - - +
644B GLU* 2.9 60.8 + - - +
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Residues in contact with GLN 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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48A CYS* 3.5 22.0 - - - -
125A MET* 2.8 41.1 - - - +
639B CYS* 3.8 4.3 - - - +
640B TRP* 1.3 116.2 + - + +
642B ASP* 1.3 57.9 + - - +
644B GLU* 3.9 3.9 - - - +
645B ARG* 3.0 47.8 + - - +
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Residues in contact with ASP 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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48A CYS* 3.8 12.5 - - - +
638B GLU* 3.9 15.6 - - + +
639B CYS* 3.2 29.6 + - - +
641B GLN* 1.3 74.8 - - - +
643B LYS* 1.3 66.2 + - - +
645B ARG* 2.6 39.2 + - - +
646B GLN* 3.0 23.4 + - - +
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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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588B LEU* 2.9 43.9 + - + +
589B SER* 4.7 0.8 - - - +
591B CYS* 4.2 10.8 - - - -
592B SER* 4.7 8.9 + - - -
627B SER* 4.0 11.7 - - - +
630B ALA* 3.9 7.9 - - + -
631B CYS* 3.4 29.8 - - - -
634B GLU* 2.9 36.5 + - - -
638B GLU* 3.2 22.7 + - - +
639B CYS 3.3 1.8 + - - -
640B TRP* 3.1 10.4 + - - +
642B ASP* 1.3 78.4 - - - +
644B GLU* 1.3 61.7 + - - +
646B GLN* 3.1 8.3 + - - +
647B LEU* 3.0 22.2 + - - +
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Residues in contact with GLU 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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588B LEU* 5.6 1.8 - - + -
613B TRP* 4.0 20.6 + - + -
623B TRP* 3.8 2.4 - - - +
624B SER* 3.4 22.5 + - - -
627B SER* 2.8 29.2 + - - +
640B TRP* 2.9 38.7 + - + +
641B GLN* 3.9 4.5 - - - +
643B LYS* 1.3 76.1 - - - +
645B ARG* 1.3 62.0 + - - +
647B LEU* 3.4 7.0 + - - +
648B ARG* 3.1 58.4 + - - +
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Residues in contact with ARG 645 (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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48A CYS* 4.8 4.2 - - - +
616B GLU* 6.1 1.6 - - - +
641B GLN* 3.0 37.0 + - - +
642B ASP* 2.6 47.9 + - - +
644B GLU* 1.3 77.9 - - - +
646B GLN* 1.3 57.7 + - - +
648B ARG* 3.8 9.2 - - - +
649B ALA* 3.1 28.3 + - - +
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Residues in contact with GLN 646 (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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591B CYS* 3.9 9.8 - - - -
592B SER* 3.5 34.0 + - - +
638B GLU* 4.4 11.7 - - - +
642B ASP 3.0 12.9 + - - +
643B LYS* 3.1 10.2 + - - +
645B ARG* 1.3 75.4 - - - +
647B LEU* 1.3 61.4 + - - +
649B ALA* 3.2 6.0 + - + +
650B ARG* 2.9 72.3 + - + +
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Residues in contact with LEU 647 (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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584B VAL* 4.1 23.3 - - + +
587B LEU* 3.9 22.7 - - + +
588B LEU* 4.1 25.1 - - + -
591B CYS* 3.6 28.4 - - + -
597B ILE* 4.0 11.2 - - + -
599B MET* 6.2 0.4 - - - -
613B TRP* 3.9 24.7 - - + -
643B LYS 3.0 14.7 + - - +
644B GLU* 3.4 5.6 + - - +
646B GLN* 1.3 76.8 - - - +
648B ARG* 1.3 56.9 + - - +
650B ARG 3.2 1.6 + - - -
651B VAL* 3.0 45.2 + - + +
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Residues in contact with ARG 648 (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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613B TRP* 2.9 69.2 + - + +
614B LEU* 3.9 28.7 + - + +
616B GLU* 3.3 43.7 - - - +
644B GLU* 3.1 53.6 + - - +
645B ARG* 3.8 7.8 - - - +
647B LEU* 1.3 77.8 - - - +
649B ALA* 1.3 62.4 + - - +
650B ARG 3.7 0.2 + - - -
651B VAL* 3.9 12.6 + - - +
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Residues in contact with ALA 649 (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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645B ARG 3.1 18.6 + - - +
646B GLN* 3.5 8.7 - - + +
647B LEU 3.2 0.2 - - - -
648B ARG* 1.3 78.9 - - - +
650B ARG* 1.3 65.0 + - + +
651B VAL 3.6 1.7 + - - +
652B LYS* 2.8 26.0 + - - +
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Residues in contact with ARG 650 (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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591B CYS 2.7 37.2 + - - -
592B SER 3.7 10.5 + - - -
593B HIS 4.0 1.0 - - - -
594B PHE 3.1 31.7 + - - +
595B GLU* 3.6 35.3 - - - +
597B ILE* 2.8 37.1 + - + -
646B GLN* 2.9 44.5 + - + +
647B LEU* 3.2 2.9 + - - +
649B ALA* 1.3 80.5 - - + +
651B VAL* 1.3 59.7 + - - +
652B LYS* 3.1 10.6 + - - +
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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