Contacts of the helix formed by residues 634 - 643 (chain B) in PDB entry 2P0C
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 PHE 634 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B MET* 5.8 5.2 - - + -
633B GLU* 1.3 91.1 + - + +
635B LEU* 1.3 85.2 + - + +
636B SER 3.2 6.4 + - - -
637B GLU* 3.4 28.9 + - + +
638B ALA* 3.5 12.4 + - + +
655B VAL* 4.4 19.1 - - + -
657B ILE* 6.0 1.1 - - + -
667B PRO* 3.9 34.3 - - + -
669B VAL* 4.6 13.9 - - + -
743B GLY 5.8 0.7 - - - -
744B LEU 4.8 16.2 - - - -
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Residues in contact with LEU 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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577B LEU* 3.2 28.9 - - - +
578B GLU* 4.7 2.2 - - + -
580B VAL* 3.8 7.9 - - + +
581B VAL* 3.8 22.0 - - + -
633B GLU* 3.7 3.9 - - - +
634B PHE* 1.3 105.7 - - + +
636B SER* 1.3 60.4 + - - +
637B GLU 3.4 0.2 - - - -
638B ALA* 3.8 7.6 - - - -
639B ALA* 2.9 30.7 + - - +
655B VAL* 4.0 18.6 - - + -
657B ILE* 4.8 8.5 - - + -
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Residues in contact with SER 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B LEU* 6.2 1.3 - - - +
633B GLU* 4.7 15.9 - - - +
634B PHE 3.2 0.6 - - - -
635B LEU* 1.3 76.5 - - - +
637B GLU* 1.3 60.6 + - - +
639B ALA* 3.8 4.9 - - - +
640B CYS* 3.0 27.4 + - - +
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Residues in contact with GLU 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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634B PHE* 3.4 24.1 + - + +
636B SER* 1.3 78.7 + - - +
638B ALA* 1.3 56.5 + - - +
640B CYS* 3.1 8.8 + - - +
641B MET* 2.8 38.0 + - - +
719B PHE* 3.5 31.9 - - + -
743B GLY* 3.3 26.8 - - - +
744B LEU 5.1 0.7 - - - +
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Residues in contact with ALA 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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580B VAL* 3.8 10.1 - - + -
634B PHE* 3.5 17.4 + - + +
635B LEU* 4.0 9.9 - - - +
636B SER 3.4 0.2 - - - -
637B GLU* 1.3 81.0 - - - +
639B ALA* 1.3 51.8 + - - +
641B MET* 3.2 4.3 + - - +
642B LYS* 2.7 34.5 + - - +
652B LEU* 3.4 19.3 - - + +
655B VAL* 4.0 28.3 - - + -
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Residues in contact with ALA 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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577B LEU* 5.5 8.3 - - - -
579B ASP* 4.8 9.0 - - - +
580B VAL* 3.9 17.7 - - + +
635B LEU 2.9 20.7 + - - +
636B SER* 3.8 6.3 - - - +
637B GLU 3.3 0.4 - - - -
638B ALA* 1.3 73.0 - - - +
640B CYS* 1.3 64.2 + - - +
642B LYS* 3.4 6.3 + - - +
643B ASP* 3.3 28.3 + - - +
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Residues in contact with CYS 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 SER 3.0 15.6 + - - +
637B GLU* 3.1 12.5 + - - +
639B ALA* 1.3 76.6 - - - +
641B MET* 1.3 57.6 + - - +
643B ASP* 3.0 26.5 + - - +
644B PHE* 3.5 32.9 + - + -
717B ARG* 6.0 4.3 - - - -
719B PHE* 4.7 11.0 - - + -
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Residues in contact with MET 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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637B GLU* 2.8 28.5 + - - +
638B ALA* 3.5 5.8 - - - +
640B CYS* 1.3 73.4 - - - +
642B LYS* 1.3 65.1 + - - +
644B PHE* 3.1 37.3 + - + +
650B ILE 5.0 0.7 - - - +
651B ARG* 4.8 0.2 - - - -
652B LEU* 3.8 40.6 + - + -
671B LEU* 5.9 4.3 - - + -
719B PHE* 3.7 28.9 - - + -
742B PHE* 3.1 38.4 - - + +
743B GLY* 4.1 11.4 - - - +
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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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579B ASP* 3.6 33.2 + - - +
580B VAL* 4.1 16.4 - - + +
638B ALA 2.7 20.4 + - - +
639B ALA* 3.6 10.3 - - - +
641B MET* 1.3 73.9 - - - +
643B ASP* 1.3 63.2 + - - +
651B ARG* 3.4 23.3 + - - +
652B LEU* 3.4 30.5 - - + +
653B LEU* 3.9 16.4 - - - +
654B GLY* 5.4 0.2 - - - -
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Residues in contact with ASP 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 ALA* 3.3 15.5 + - - +
640B CYS* 3.0 16.0 + - - +
642B LYS* 1.3 80.2 - - - +
644B PHE* 1.3 58.6 + - + +
645B SER* 3.0 15.1 + - - -
651B ARG* 4.7 3.6 + - - +
713B TYR* 3.8 5.0 + - - -
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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