Contacts of the helix formed by residues 634 - 643 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A MET* 4.2 18.6 - - + -
633A GLU* 1.3 86.4 + - - +
635A LEU* 1.3 84.0 + - + +
636A SER 3.4 0.4 - - - -
637A GLU* 3.7 13.3 + - + +
638A ALA* 3.7 16.8 + - + +
655A VAL* 4.2 15.3 - - + -
657A ILE* 5.9 0.9 - - + -
667A PRO* 3.7 33.0 - - + -
669A VAL* 4.0 28.9 - - + -
744A LEU* 4.5 18.8 - - + -
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Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A LEU* 4.1 13.0 - - - +
578A GLU* 5.8 0.4 - - - -
580A VAL* 3.9 9.4 - - + +
581A VAL* 3.9 22.4 - - + -
633A GLU* 2.8 11.7 + - - +
634A PHE* 1.3 95.1 - - + +
636A SER* 1.3 52.5 + - - +
638A ALA* 3.1 6.9 + - - +
639A ALA* 2.7 36.6 + - - +
655A VAL* 3.7 27.6 - - + -
657A ILE* 4.6 15.3 - - + -
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Residues in contact with SER 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A LEU* 6.4 1.1 - - - +
633A GLU* 2.6 31.3 + - - -
635A LEU* 1.3 72.5 - - - +
637A GLU* 1.3 57.0 + - - +
639A ALA* 3.3 7.7 + - - +
640A CYS* 2.9 27.7 + - - +
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Residues in contact with GLU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A GLU* 4.5 0.2 + - - -
634A PHE* 3.7 13.9 + - + +
635A LEU 3.4 0.4 - - - -
636A SER* 1.3 78.4 + - - +
638A ALA* 1.3 53.7 + - - +
640A CYS* 3.2 7.6 + - - +
641A MET* 2.8 39.0 + - - +
719A PHE* 3.8 27.9 - - + -
743A GLY* 3.0 28.9 - - - +
744A LEU 3.2 15.6 - - - +
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Residues in contact with ALA 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A VAL* 3.7 8.1 - - + -
634A PHE* 3.7 16.6 + - + +
635A LEU* 3.1 11.1 + - - +
637A GLU* 1.3 79.7 - - - +
639A ALA* 1.3 51.5 + - - +
641A MET* 3.4 7.3 + - - -
642A LYS* 2.8 30.3 + - - +
652A LEU* 3.1 19.3 - - + +
655A VAL* 3.9 28.9 - - + -
669A VAL* 5.9 0.7 - - + -
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Residues in contact with ALA 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A LEU* 5.0 12.8 - - - -
579A ASP* 6.5 0.4 - - + -
580A VAL* 3.7 21.9 - - + +
635A LEU 2.7 19.5 + - - +
636A SER* 3.6 9.2 - - - +
638A ALA* 1.3 70.2 - - - +
640A CYS* 1.3 66.9 + - - +
642A LYS* 3.3 15.9 + - - +
643A ASP* 3.4 15.5 + - - +
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Residues in contact with CYS 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636A SER 2.9 14.3 + - - +
637A GLU* 3.3 13.0 - - - +
639A ALA* 1.3 76.5 - - - +
641A MET* 1.3 61.5 + - - +
643A ASP* 3.1 22.3 + - - +
644A PHE* 3.8 24.7 + - - -
719A PHE* 4.5 12.1 - - + -
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Residues in contact with MET 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A GLU* 2.8 29.8 + - - +
638A ALA* 3.7 8.5 - - - +
640A CYS* 1.3 70.4 - - - +
642A LYS* 1.3 65.3 + - - +
644A PHE* 3.2 37.2 + - + +
650A ILE 5.3 0.5 - - - +
652A LEU* 4.0 38.9 + - + +
669A VAL* 6.4 0.2 - - + -
671A LEU* 5.7 3.1 - - + -
719A PHE* 3.5 31.2 - - + -
742A PHE* 3.7 32.8 - - + +
743A GLY* 4.1 10.1 - - - -
744A LEU 4.6 7.4 - - - +
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Residues in contact with LYS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A ASP* 2.7 35.5 + - + +
580A VAL* 3.5 25.1 + - + +
582A ILE* 5.4 3.0 - - - +
638A ALA 2.8 20.2 + - - +
639A ALA* 3.4 9.9 - - - +
640A CYS 3.2 0.4 - - - -
641A MET* 1.3 72.8 - - - +
643A ASP* 1.3 64.3 + - - +
644A PHE 3.5 6.2 + - - +
651A ARG* 5.8 1.0 - - - +
652A LEU* 3.6 28.8 + - + +
653A LEU* 3.4 22.4 + - - +
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Residues in contact with ASP 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ALA 3.8 11.9 - - - +
640A CYS* 3.1 13.2 + - - +
641A MET 3.1 1.0 - - - -
642A LYS* 1.3 83.2 - - - +
644A PHE* 1.3 64.6 + - + +
645A SER* 3.5 7.8 + - - -
713A TYR* 4.2 2.9 + - - -
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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