Contacts of the strand formed by residues 631 - 637 (chain B) in PDB entry 4K8R
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 THR 631 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455B LEU* 2.9 36.9 + - - +
457B CYS* 3.8 35.0 - - + +
525B ARG* 4.8 0.9 - - - +
626B CYS* 4.1 2.5 - - - -
629B GLY 4.3 5.0 + - - -
630B TRP* 1.3 73.4 - - - +
632B LEU* 1.3 63.8 + - - +
633B THR* 3.4 1.7 + - - +
652B ASN* 3.6 13.1 + - - +
678B CYS* 3.5 0.9 - - - -
679B CYS* 2.8 45.0 + - - +
680B ARG* 5.4 0.9 - - - +
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Residues in contact with LEU 632 (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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457B CYS* 3.7 6.9 - - - +
525B ARG* 2.7 31.6 + - - +
626B CYS* 3.6 16.1 - - - -
631B THR* 1.3 69.7 - - - +
633B THR* 1.3 56.1 + - - +
634B GLY 3.4 29.6 - - - +
635B CYS* 4.1 1.6 - - + +
649B ALA* 3.7 25.4 - - + -
651B ASP 4.7 0.2 - - - +
652B ASN* 2.9 25.4 + - - +
653B THR 3.6 13.2 - - - +
654B CYS* 3.5 31.0 - - + +
676B ALA* 3.9 13.2 - - + -
677B ILE 3.4 16.4 - - - +
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Residues in contact with THR 633 (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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455B LEU* 3.9 11.4 - - + -
457B CYS* 3.9 5.2 - - - -
484B LEU* 3.6 31.0 - - + -
485B SER* 2.7 28.8 + - - -
525B ARG* 3.1 20.2 - - - +
560B THR 2.9 21.3 + - - -
631B THR 3.4 4.5 + - - +
632B LEU* 1.3 78.5 - - - +
634B GLY* 1.3 52.0 + - - +
635B CYS 4.3 0.2 - - - -
677B ILE* 2.8 17.3 + - - +
679B CYS* 3.2 35.2 - - + -
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Residues in contact with GLY 634 (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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485B SER* 3.4 14.8 - - - -
560B THR 3.5 6.7 + - - -
561B GLY* 4.3 0.9 - - - -
562B CYS 5.5 0.4 - - - -
632B LEU* 3.4 5.3 - - - +
633B THR* 1.3 80.3 + - - +
635B CYS* 1.3 60.8 + - - -
675B VAL 3.5 2.3 - - - +
676B ALA* 3.4 3.3 - - - -
677B ILE* 2.7 47.6 + - - +
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Residues in contact with CYS 635 (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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485B SER* 4.1 6.0 + - - -
486B CYS 5.2 0.7 - - - +
487B SER* 4.3 18.1 - - - +
525B ARG* 5.9 0.4 - - - +
562B CYS 5.0 5.9 - - - +
632B LEU* 4.1 2.8 - - + +
633B THR 4.3 0.4 - - - -
634B GLY* 1.3 71.8 - - - -
636B SER* 1.3 62.6 + - - +
647B ALA* 4.2 3.7 - - - +
648B TYR* 3.4 20.9 - - - -
649B ALA* 3.9 24.1 - - + +
654B CYS* 2.0 58.8 - - + -
655B VAL 3.4 11.4 - - - -
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Residues in contact with SER 636 (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 CYS* 5.1 18.7 - - - +
634B GLY 5.1 0.9 - - - -
635B CYS* 1.3 76.1 - - - +
637B ALA* 1.3 70.1 + - - +
638B LEU* 5.1 0.2 - - - -
639B PRO* 5.4 1.0 - - - +
647B ALA* 4.1 10.1 - - - -
654B CYS* 3.2 6.6 - - - -
656B VAL* 3.7 0.3 - - - +
674B ALA* 3.6 4.2 - - - -
675B VAL* 2.7 53.0 + - - +
677B ILE* 5.4 4.7 - - - -
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Residues in contact with ALA 637 (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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495B ARG* 5.3 5.2 - - - +
636B SER* 1.3 81.9 + - - +
638B LEU* 1.3 67.2 + - - +
639B PRO* 3.3 8.1 - - - +
644B VAL* 4.2 15.3 - - + -
647B ALA* 4.0 9.6 - - + +
656B VAL* 3.5 30.1 - - + -
672B VAL* 5.7 0.9 - - + -
673B THR 3.6 5.6 - - - +
675B VAL* 4.5 0.4 - - - -
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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