Contacts of the strand formed by residues 641 - 646 (chain B) in PDB entry 4RS6
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 TYR 641 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474B THR* 3.1 29.9 - - + +
475B VAL* 5.0 13.6 - - + +
478B VAL* 3.8 34.5 - - + -
619B GLY* 6.0 1.1 - - - -
634B ILE* 4.1 15.3 - - + -
635B CYS* 3.5 13.7 - - - -
636B SER* 3.9 20.6 - - - -
639B GLU 5.8 1.8 - - - -
640B GLU* 1.3 82.4 - - - +
642B LEU* 1.3 63.7 + - - +
656B ARG* 3.8 1.4 - - - +
657B LEU* 3.1 44.0 + - + +
658B THR 4.9 0.3 + - - -
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Residues in contact with LEU 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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497B LEU* 4.2 16.2 - - + -
499B THR* 4.1 20.4 - - + +
501B PHE* 6.1 1.3 - - + -
633B ILE 4.4 0.2 - - - -
634B ILE* 3.2 10.0 - - - +
635B CYS* 2.7 41.9 + - - +
637B GLN* 3.9 29.8 - - + +
640B GLU* 4.2 13.2 - - + +
641B TYR* 1.3 81.8 - - - +
643B LEU* 1.3 61.8 + - - +
644B THR* 4.3 1.1 - - + -
654B THR* 4.3 13.9 - - + -
655B PHE 3.4 6.3 - - - +
656B ARG* 3.8 27.8 - - + +
657B LEU* 4.4 2.5 - - - +
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Residues in contact with LEU 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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632B ILE* 3.8 17.5 - - + -
633B ILE 3.2 5.8 - - - -
634B ILE* 3.6 26.5 - - + -
642B LEU* 1.3 75.8 - - - +
644B THR* 1.3 80.4 + - - +
645B TYR* 3.9 6.1 - - + +
654B THR* 3.5 0.6 - - - -
655B PHE* 2.8 42.2 + - + +
657B LEU* 3.9 21.3 - - + -
660B LEU* 3.8 18.6 - - + -
669B LEU* 4.6 11.4 - - + -
673B MET* 4.3 22.0 - - + -
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Residues in contact with THR 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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501B PHE* 3.6 34.7 - - + -
631B LYS 3.9 0.3 - - - +
632B ILE* 3.4 3.1 - - - -
633B ILE* 2.7 54.6 + - + +
635B CYS* 5.9 2.9 - - - -
642B LEU* 5.8 1.3 - - + -
643B LEU* 1.3 81.7 - - - +
645B TYR* 1.3 60.5 + - - +
646B ILE* 3.9 12.0 - - - +
652B SER* 4.3 2.5 - - - -
653B THR 3.2 6.0 + - - -
654B THR* 3.0 34.5 - - + +
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Residues in contact with TYR 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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492B ILE* 4.7 12.6 - - + -
630B THR* 3.7 5.9 - - - +
631B LYS 3.3 14.6 - - - -
632B ILE* 4.3 2.5 - - + +
643B LEU* 3.9 1.4 - - - +
644B THR* 1.3 72.4 - - - +
646B ILE* 1.3 71.2 + - - +
647B ASN* 3.8 24.5 - - + -
648B GLU* 3.6 7.3 + - - -
651B ILE 3.7 1.6 - - - +
652B SER* 3.3 1.2 - - - -
653B THR* 2.7 49.8 + - - +
655B PHE* 4.6 5.2 - - + -
668B GLU* 3.0 39.6 + - + +
669B LEU* 3.7 41.3 - - + -
672B ARG* 3.5 33.1 + - - -
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Residues in contact with ILE 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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501B PHE* 5.3 2.5 - - + -
503B TRP* 4.3 28.7 - - + -
629B HIS 4.9 6.5 - - - +
630B THR* 3.1 9.9 - - - -
631B LYS* 2.8 51.0 + - + +
633B ILE* 4.1 22.0 - - + -
644B THR* 3.9 6.7 - - - +
645B TYR* 1.3 80.7 - - - +
647B ASN* 1.3 66.8 + - - +
650B ARG* 3.7 29.4 - - + +
651B ILE 3.5 3.4 - - - +
652B SER* 3.8 19.7 - - - -
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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