Contacts of the strand formed by residues 682 - 687 (chain A) in PDB entry 4I1R
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 LEU 682 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A MET* 3.9 10.8 - - + -
614A ILE* 5.0 0.9 - - + -
635A PHE* 4.1 16.2 - - + -
636A PRO* 3.7 23.8 - - + -
639A LEU* 4.6 2.0 - - + -
672A LEU* 3.6 25.8 - - + -
675A LEU* 5.6 0.7 - - + -
678A LEU* 3.8 21.9 - - + +
680A GLU 3.5 1.6 + - - -
681A HIS* 1.3 68.7 - - - +
683A VAL* 1.3 62.6 + - - +
684A PHE* 4.4 9.6 - - + -
705A VAL 3.5 0.9 - - - +
706A ASN* 3.3 6.6 - - - +
707A VAL* 2.9 54.2 + - + +
708A GLY 2.7 19.8 + - - +
710A PRO* 4.0 7.9 - - + -
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Residues in contact with VAL 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ASP 3.4 7.8 - - - +
636A PRO* 3.3 28.2 - - + +
680A GLU* 6.2 0.9 - - + -
681A HIS* 3.2 12.0 + - + +
682A LEU* 1.3 78.0 - - - +
684A PHE* 1.3 64.1 + - - +
685A THR* 5.9 0.2 - - - +
704A GLU* 3.5 40.8 - - + +
705A VAL 3.3 6.5 - - - +
706A ASN* 3.6 20.4 - - + +
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Residues in contact with PHE 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A LEU* 3.7 23.6 - - + -
604A PHE* 5.0 0.4 - + - -
614A ILE* 4.8 9.6 - - + -
632A VAL* 3.6 27.1 - - + -
633A THR 3.4 11.0 - - - +
634A ASP 3.7 4.5 - - - -
635A PHE* 3.6 32.1 - + + -
682A LEU* 4.4 11.2 - - + -
683A VAL* 1.3 77.2 - - - +
685A THR* 1.3 68.9 + - - +
686A VAL* 3.6 23.3 - - + -
703A GLN 4.0 0.3 - - - +
704A GLU* 3.6 2.8 - - - -
705A VAL* 3.0 55.9 + - + +
707A VAL* 4.1 18.2 - - + -
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Residues in contact with THR 685 (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 VAL* 3.7 2.6 - - - -
633A THR* 2.8 48.8 + - + +
634A ASP* 4.0 17.5 + - - +
683A VAL* 5.9 0.3 - - - +
684A PHE* 1.3 76.5 - - - +
686A VAL* 1.3 62.4 + - - +
702A LYS* 3.6 37.7 - - + -
703A GLN 3.4 17.9 - - - +
704A GLU* 4.3 9.7 - - + +
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Residues in contact with VAL 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A LEU* 4.3 15.9 - - + -
594A PHE* 4.0 15.0 - - + -
600A ILE* 4.9 5.2 - - + -
602A LEU* 4.0 13.7 - - + -
616A THR* 5.2 0.4 - - + -
630A ALA* 3.8 25.4 - - + -
631A TYR 3.2 14.8 - - - +
632A VAL* 3.9 9.4 - - + -
684A PHE* 3.6 30.7 - - + -
685A THR* 1.3 71.9 - - - +
687A CYS* 1.3 61.4 + - - +
701A ASP 3.7 1.2 - - - +
702A LYS* 3.3 22.2 - - - -
703A GLN 3.2 15.3 + - - +
705A VAL* 4.5 2.7 - - + -
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Residues in contact with CYS 687 (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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594A PHE* 5.5 0.4 - - - -
629A ASP 3.6 0.5 - - - +
630A ALA* 3.2 6.0 - - - -
631A TYR* 2.9 42.7 + - + +
633A THR* 5.3 8.9 - - + +
685A THR 4.3 0.2 - - - -
686A VAL* 1.3 73.3 - - - +
688A LEU* 1.4 60.5 + - - +
689A SER* 4.9 1.6 - - - +
700A GLU* 3.8 37.5 - - + -
701A ASP 3.5 14.1 - - - -
702A LYS* 3.8 22.2 - - + -
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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