Contacts of the strand formed by residues 641 - 646 (chain B) in PDB entry 3A98
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 ALA 641 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618B THR* 3.4 2.9 - - - -
619B GLY 3.1 21.5 + - - +
622B CYS* 3.7 8.3 - - - -
624B HIS* 4.1 9.6 - - + -
625B MSE 3.8 16.8 - - + -
637B VAL 2.9 12.7 + - - +
638B LEU 3.3 7.8 + - - +
640B LEU* 1.3 77.8 - - - +
642B PHE* 1.3 62.2 + - - +
654B PHE 3.6 5.2 - - - -
655B ILE* 3.7 16.8 - - + -
662B TYR* 3.5 7.6 - - - -
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Residues in contact with PHE 642 (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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562B PHE* 3.9 4.3 - + - -
616B VAL* 4.8 4.0 - - + -
617B VAL 3.1 13.0 - - - +
618B THR* 4.0 12.6 - - + -
622B CYS* 3.5 2.4 - - - -
640B LEU 3.8 9.6 - - - -
641B ALA* 1.3 74.1 - - - +
643B SER* 1.3 65.4 + - - +
654B PHE* 3.0 75.9 + + + +
656B ALA* 4.0 22.4 - - + -
662B TYR* 3.8 14.1 - + + -
665B TRP* 3.5 36.3 - + + -
666B THR* 4.2 10.3 - - + -
669B LEU* 4.2 20.0 - - + -
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Residues in contact with SER 643 (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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616B VAL* 3.1 9.0 - - - +
617B VAL* 2.7 50.4 + - - +
622B CYS* 3.6 1.2 - - - -
623B PRO* 3.4 8.5 - - - +
624B HIS* 2.9 22.2 + - - -
642B PHE* 1.3 72.5 + - - +
644B ILE* 1.3 64.7 + - - +
645B LEU* 3.7 7.2 + - - -
652B LEU 3.4 4.7 - - - -
653B ASN* 2.7 29.2 + - - -
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Residues in contact with ILE 644 (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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586B LEU* 3.5 28.9 - - + -
608B LEU* 3.6 23.3 - - + -
613B ILE* 3.9 31.9 - - + -
615B ALA 3.6 2.7 - - - -
616B VAL* 4.6 2.0 - - + +
642B PHE* 5.2 0.2 - - + -
643B SER* 1.3 72.7 - - - +
645B LEU* 1.3 63.6 + - - +
646B TYR* 3.5 5.0 - - + -
651B GLN* 3.3 2.8 - - - -
652B LEU* 2.9 35.0 + - + +
654B PHE* 3.7 26.9 - - + -
665B TRP* 5.7 0.7 - - + -
669B LEU* 3.8 33.7 - - + -
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Residues in contact with LEU 645 (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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613B ILE* 3.8 2.1 - - - +
614B LYS* 2.9 25.2 + - + -
615B ALA* 2.8 29.9 + - + +
617B VAL* 3.7 31.9 - - + -
623B PRO* 4.7 5.8 - - + -
643B SER* 4.4 14.8 - - - +
644B ILE* 1.3 71.9 - - - +
646B TYR* 1.3 61.4 + - - +
650B CYS 3.6 5.4 - - - +
651B GLN* 3.7 28.0 - - + +
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Residues in contact with TYR 646 (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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588B TYR* 4.4 9.2 + - - -
605B GLN* 4.1 17.7 + - - -
607B LYS 4.7 4.6 + - - -
608B LEU* 3.4 51.0 - - + +
609B PRO* 5.6 2.5 - - + -
612B ASP* 3.0 25.6 - - + +
613B ILE* 3.8 4.5 - - + -
614B LYS* 4.0 5.2 - - - +
644B ILE 3.5 10.1 - - - -
645B LEU* 1.3 75.4 - - - +
647B ASP* 1.3 99.7 + - - +
648B SER 3.4 2.3 + - - +
650B CYS* 3.1 46.9 + - + +
651B GLN* 3.8 13.5 + - - -
652B LEU* 4.0 4.9 - - + +
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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