Contacts of the strand formed by residues 649 - 652 (chain B) in PDB entry 3I8E
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 649 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592B LEU* 3.8 17.7 - - + -
594B THR* 3.4 33.7 - - + +
596B PHE* 4.0 10.3 - - + -
603B LEU* 5.6 5.2 - - + -
638B LEU* 4.2 14.1 - - + -
639B ARG 3.3 11.7 - - - +
640B THR* 3.8 13.7 - - + +
641B PHE* 3.6 4.0 - - - -
648B ASN* 1.3 82.5 - - - +
650B PHE* 1.3 65.7 + - - +
659B ILE* 2.7 50.9 + - + +
666B LEU* 6.4 0.4 - - + -
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Residues in contact with PHE 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B VAL 3.4 3.3 - - - +
638B LEU* 3.7 1.6 - - - -
639B ARG 2.6 32.2 + - - -
641B PHE* 3.7 10.8 - - + -
649B VAL* 1.3 73.8 - - - +
651B ALA* 1.3 68.7 + - - +
652B CYS* 3.3 30.3 - - - -
656B PRO* 4.0 14.8 - - + -
657B THR 3.7 3.4 - - - -
658B VAL* 3.5 26.9 - - + +
671B VAL* 4.4 16.6 - - + -
676B VAL* 3.7 13.7 - - + -
679B MET* 3.3 35.9 - - + -
691B LEU* 5.0 8.3 - - + -
693B LEU* 3.7 28.5 - - + -
704B ILE* 6.1 3.1 - - + -
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Residues in contact with ALA 651 (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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631B LEU* 3.8 17.3 - - + -
636B THR* 3.7 19.3 - - + -
637B VAL 3.5 4.3 - - - -
638B LEU* 3.9 15.5 - - + -
649B VAL 4.1 0.2 + - - -
650B PHE* 1.3 76.4 - - - +
652B CYS* 1.3 62.6 + - - +
653B SER* 4.7 0.3 + - - -
655B ARG 4.4 0.9 - - - +
656B PRO* 3.5 2.3 - - - +
657B THR* 2.6 46.1 + - - +
659B ILE* 4.3 8.1 - - + -
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Residues in contact with CYS 652 (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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635B PRO 3.8 0.9 - - - +
636B THR* 3.1 21.7 - - - +
637B VAL* 3.0 23.6 + - + +
639B ARG* 5.8 2.7 - - - -
650B PHE* 3.3 29.4 - - + -
651B ALA* 1.3 70.7 - - - +
653B SER* 1.3 67.6 + - - +
656B PRO* 4.7 2.5 - - - -
676B VAL* 3.2 22.0 - - - +
677B ASN* 3.4 27.1 - - - +
678B TYR* 4.0 9.9 - - - -
679B MET* 4.1 5.4 - - - -
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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