Contacts of the helix formed by residues 633 - 643 (chain A) in PDB entry 3FA2
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 633 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A LEU* 3.7 19.7 - - + -
581A GLN* 3.4 61.0 - - + +
584A MET* 3.5 40.4 - - + -
585A LEU* 4.8 1.6 - - + -
608A VAL* 3.7 13.2 - - + -
609A VAL 3.1 15.0 + - - +
610A PRO 3.7 16.9 + - - +
632A LYS* 1.3 69.4 - - - +
634A GLU* 1.3 62.3 + - - +
635A TRP 3.0 5.4 - - - -
636A VAL* 3.1 31.6 + - + -
637A LYS* 3.2 16.9 + - + +
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Residues in contact with GLU 634 (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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632A LYS* 3.6 39.0 + - + +
633A PHE* 1.3 76.1 - - - +
635A TRP* 1.3 54.5 + - - +
636A VAL 3.4 0.2 - - - -
637A LYS* 3.6 22.8 - - + +
638A ALA* 3.1 22.2 + - - +
641A ARG* 4.8 1.4 + - - -
650A LYS* 4.7 10.8 - - - +
651A TYR* 3.4 29.8 - - + -
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Residues in contact with TRP 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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570A LEU* 4.5 4.3 - - + -
572A LEU* 4.2 15.0 - - + -
588A LEU* 3.8 24.7 - - + -
592A LEU* 4.6 1.6 - - + -
606A HIS* 3.6 31.6 - + - -
608A VAL* 4.2 18.2 - - + -
631A LEU* 3.5 22.0 - - + -
632A LYS 3.2 15.9 + - - +
633A PHE 3.0 0.6 - - - -
634A GLU* 1.3 76.3 - - - +
636A VAL* 1.3 77.5 + - + +
638A ALA* 3.5 2.4 + - - +
639A CYS* 3.0 44.6 + - - -
645A CYS* 4.3 11.4 - - - -
646A GLU* 3.0 26.9 + - + -
647A GLN 4.4 1.1 - - - -
648A GLU* 4.0 4.9 - - + +
651A TYR* 3.3 47.1 - + + -
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Residues in contact with VAL 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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584A MET 4.0 9.4 - - - +
585A LEU* 3.3 30.3 - - + -
588A LEU* 4.2 6.5 - - + -
608A VAL* 3.9 11.2 - - + -
633A PHE* 3.1 32.6 + - + +
635A TRP* 1.3 91.3 - - + +
637A LYS* 1.3 67.9 + - - +
639A CYS* 3.1 5.5 + - - +
640A LEU* 2.9 49.2 + - + +
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Residues in contact with LYS 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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584A MET* 4.3 14.1 - - + -
633A PHE* 3.5 28.3 - - + +
634A GLU* 3.6 25.6 - - + +
636A VAL* 1.3 80.2 - - - +
638A ALA* 1.3 52.5 + - - +
640A LEU* 3.2 3.9 + - - +
641A ARG* 2.8 61.3 + - - +
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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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634A GLU 3.1 12.2 + - - +
635A TRP 3.7 4.9 - - - +
637A LYS* 1.3 79.8 - - - +
639A CYS* 1.3 62.4 + - - +
641A ARG* 3.3 22.3 - - - +
642A ARG* 3.1 25.6 + - - +
646A GLU* 3.7 15.9 - - + +
651A TYR* 3.2 28.0 - - + +
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Residues in contact with CYS 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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588A LEU* 3.1 28.7 - - + +
592A LEU* 4.7 0.2 - - - -
635A TRP* 3.0 62.2 + - - -
636A VAL 3.1 5.3 + - - +
638A ALA* 1.3 74.6 - - - +
640A LEU* 1.3 54.3 + - - +
643A LYS* 2.5 37.6 + - - -
644A VAL 3.3 14.2 + - - +
645A CYS* 4.4 2.0 - - - -
646A GLU* 3.6 20.6 - - - -
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Residues in contact with LEU 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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584A MET* 3.7 44.0 - - + +
587A GLU* 5.0 15.5 - - + +
588A LEU* 3.2 44.0 - - + +
591A ILE* 5.3 8.8 - - + +
636A VAL* 2.9 28.7 + - + +
637A LYS* 3.7 4.7 - - - +
639A CYS* 1.3 72.3 - - - +
641A ARG* 1.3 67.5 + - - +
642A ARG 3.1 0.7 + - - -
643A LYS* 3.4 22.3 + - - +
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Residues in contact with ARG 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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634A GLU 4.8 1.6 + - - -
637A LYS* 2.8 52.8 + - - +
638A ALA* 3.3 34.8 - - - +
640A LEU* 1.3 77.5 - - - +
642A ARG* 1.3 73.1 + - + +
643A LYS* 5.5 0.3 - - - +
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Residues in contact with ARG 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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638A ALA 3.1 16.3 + - - +
640A LEU 3.1 0.4 - - - -
641A ARG* 1.3 92.2 + - + +
643A LYS* 1.3 71.9 + - - +
644A VAL* 3.3 30.2 + - + +
646A GLU* 4.0 14.4 - - - +
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Residues in contact with LYS 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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591A ILE* 4.4 43.3 - - + +
592A LEU* 4.9 1.5 - - - +
639A CYS 2.5 17.8 + - - -
640A LEU 3.4 13.4 + - - +
641A ARG 5.5 0.4 - - - +
642A ARG* 1.3 75.8 - - - +
644A VAL* 1.3 59.4 + - - +
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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