Contacts of the strand formed by residues 637 - 642 (chain A) in PDB entry 3I7L
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 VAL 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A ARG* 3.3 41.5 - - - +
590A SER* 3.9 7.9 - - - +
635A PRO 3.7 3.1 + - - +
636A THR* 1.3 76.8 - - - +
638A LEU* 1.3 71.3 + - - +
639A ARG* 5.5 0.2 - - - +
650A PHE 3.8 0.7 - - - +
651A ALA* 3.6 0.5 - - - -
652A CYS* 2.6 44.1 + - + +
677A ASN 3.9 19.5 - - - +
678A TYR* 4.3 20.2 - - + -
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Residues in contact with LEU 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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590A SER* 3.8 30.7 + - - +
591A ILE 5.8 0.4 - - - +
592A LEU* 3.8 35.0 - - + +
603A LEU* 4.2 17.5 - - + +
605A ALA* 4.6 4.9 - - + -
611A LEU* 4.0 28.3 - - + -
636A THR* 4.5 4.3 - - + -
637A VAL* 1.3 85.4 - - - +
639A ARG* 1.3 65.1 + - - +
649A VAL* 3.9 17.7 - - + -
650A PHE 3.6 2.5 - - - -
651A ALA* 4.1 17.3 - - + -
659A ILE* 4.6 1.8 - - + -
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Residues in contact with ARG 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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410A LEU 3.7 10.3 + - - -
411A TRP* 3.9 11.5 - - - +
412A PRO* 3.6 29.9 - - - +
459A PHE* 6.2 1.0 - - - -
592A LEU* 4.4 6.2 - - - +
637A VAL 5.5 0.2 - - - +
638A LEU* 1.3 80.9 - - - +
640A THR* 1.3 76.1 + - - +
649A VAL* 3.2 7.2 - - - +
650A PHE 2.7 35.2 + - - +
652A CYS* 6.6 0.4 - - - -
679A MET* 3.7 38.6 + - + +
680A CYS* 3.7 10.6 - - - +
681A PRO* 3.3 25.0 - - - +
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Residues in contact with THR 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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592A LEU* 4.0 10.7 - - - +
594A THR* 3.4 32.7 - - + +
595A THR* 5.4 1.3 - - - +
639A ARG* 1.3 98.2 + - - +
641A PHE* 1.3 67.5 + - - +
647A THR* 4.1 22.9 - - + -
648A ASN 3.3 14.8 - - - +
649A VAL* 4.4 1.1 - - - +
681A PRO* 3.5 7.8 - - - +
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Residues in contact with PHE 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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640A THR* 1.3 78.2 - - - +
642A ARG* 1.3 61.8 + - - +
643A SER* 3.8 31.6 - - - -
647A THR* 3.3 3.3 - - - -
648A ASN* 2.8 68.5 + - + +
649A VAL 4.0 1.8 - - - -
650A PHE* 3.8 30.5 - + + -
658A VAL* 4.2 22.2 - - + -
660A TYR* 4.9 2.7 - - - -
679A MET* 4.0 10.3 - - + -
681A PRO* 3.7 22.0 - - + -
691A LEU* 4.2 15.0 - - + -
704A ILE* 4.4 20.2 - - + -
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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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641A PHE* 1.3 75.5 - - - +
643A SER* 1.3 61.6 + - - +
644A LEU 3.3 15.9 + - - +
645A SER* 3.3 21.5 - - - +
646A THR 3.1 18.4 - - - +
647A THR* 3.6 17.3 - - + -
681A PRO* 5.2 5.3 - - - +
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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