Contacts of the helix formed by residues 641 - 658 (chain B) in PDB entry 6WCZ
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 LYS 641 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639B LEU* 5.1 1.3 - - - -
640B ARG* 1.3 119.0 - - - +
642B PRO* 1.3 67.9 - - + +
643B GLU* 3.3 25.0 - - + +
644B LYS* 3.2 58.2 - - + +
645B VAL* 4.0 5.2 - - - +
647B ARG* 3.7 16.7 - - - +
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Residues in contact with PRO 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ILE* 4.5 16.4 - - + -
639B LEU* 4.3 23.1 - - + -
640B ARG 4.6 0.2 - - - +
641B LYS* 1.3 83.9 - - + +
643B GLU* 1.3 59.1 + - - +
645B VAL* 3.2 10.9 - - + +
646B THR* 2.9 36.6 + - + +
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Residues in contact with GLU 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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641B LYS* 3.2 18.4 + - + +
642B PRO* 1.3 80.8 - - + +
644B LYS* 1.3 58.0 + - - +
646B THR* 3.3 9.0 - - - +
647B ARG* 2.8 60.4 + - + +
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Residues in contact with LYS 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B VAL* 4.0 30.9 + - + +
631B LEU* 4.7 6.9 - - + +
632B GLU* 5.7 0.6 + - - -
635B ASP* 3.0 27.7 + - - -
640B ARG* 3.6 38.0 - - - +
641B LYS* 3.2 37.3 + - + +
643B GLU* 1.3 77.2 - - - +
645B VAL* 1.3 71.2 + - + +
647B ARG* 3.7 13.6 - - - +
648B TRP* 2.9 27.4 + - - +
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Residues in contact with VAL 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 6.2 6.3 - - + -
377B ILE* 3.8 35.0 - - + -
378B VAL* 5.7 4.3 - - + -
625B MET* 3.7 28.3 - - + -
631B LEU* 5.1 4.5 - - + -
641B LYS 4.0 2.7 - - - +
642B PRO* 3.2 21.1 - - + +
644B LYS* 1.3 91.9 - - + +
646B THR* 1.3 62.6 + - - +
647B ARG 3.1 1.3 - - - -
648B TRP* 3.9 4.7 - - - +
649B LEU* 2.9 37.7 + - + +
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Residues in contact with THR 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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377B ILE* 4.5 17.5 - - + -
381B TRP* 5.8 4.0 - - + -
642B PRO* 2.9 27.0 + - + +
643B GLU* 3.3 13.7 + - - +
645B VAL* 1.3 78.0 - - - +
647B ARG* 1.3 56.7 + - - +
649B LEU* 4.4 7.4 - - + -
650B GLN* 2.9 49.3 + - - +
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Residues in contact with ARG 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LYS* 3.7 18.0 - - - +
643B GLU* 2.8 67.8 + - + +
644B LYS* 3.7 10.4 - - - +
646B THR* 1.3 76.3 + - - +
648B TRP* 1.3 53.6 + - - +
650B GLN* 3.7 2.4 - - - -
651B SER* 2.7 47.5 + - - +
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Residues in contact with TRP 648 (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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621B LEU* 4.0 16.4 - - + -
624B ASN* 4.3 3.4 - - + -
625B MET* 3.5 44.6 - - + -
628B GLU* 2.4 40.5 + - - -
630B VAL* 3.5 32.4 - - + +
644B LYS 2.9 19.7 + - - +
645B VAL* 3.3 6.5 + - - +
647B ARG* 1.3 76.3 - - - +
649B LEU* 1.3 71.4 + - + +
652B ASN* 2.5 57.3 + - + +
653B GLY* 3.4 12.1 + - - -
656B ARG* 3.3 35.7 - - + -
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Residues in contact with LEU 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ILE* 4.5 7.2 - - + -
378B VAL* 4.0 26.2 - - + -
381B TRP* 3.5 71.9 - - + +
621B LEU* 4.8 8.7 - - + -
645B VAL* 2.9 23.9 + - + +
646B THR* 3.9 5.8 - - + +
648B TRP* 1.3 86.7 - - + +
650B GLN* 1.3 58.8 + - - +
651B SER 3.0 1.1 - - - -
652B ASN 2.8 18.0 + - - -
653B GLY* 2.9 21.7 + - - +
654B TRP 4.5 1.0 + - - -
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Residues in contact with GLN 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B TRP* 3.9 30.0 - - + +
646B THR* 2.9 35.9 + - - +
647B ARG* 3.7 2.7 - - - +
649B LEU* 1.3 71.7 - - + +
651B SER* 1.3 56.3 + - - +
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Residues in contact with SER 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B ARG* 2.7 23.4 + - - +
649B LEU 3.6 0.2 - - - -
650B GLN* 1.3 79.8 - - - +
652B ASN* 1.3 91.5 + - - +
655B ASP* 5.1 4.7 - - - +
656B ARG* 5.3 0.2 + - - -
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Residues in contact with ASN 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B TRP* 2.5 42.7 + - + +
649B LEU 2.8 5.3 + - - -
651B SER* 1.3 106.5 + - - +
653B GLY* 1.3 52.0 + - - +
654B TRP 3.4 1.6 - - - -
655B ASP* 2.8 28.4 + - - +
656B ARG* 2.9 56.8 + - - +
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Residues in contact with GLY 653 (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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381B TRP* 4.8 2.9 - - - -
621B LEU* 3.9 4.5 - - - +
648B TRP* 3.4 10.2 + - - -
649B LEU* 2.9 34.7 + - - -
652B ASN* 1.3 74.4 - - - +
654B TRP* 1.3 61.8 + - - +
656B ARG* 3.2 8.8 + - - +
657B LEU* 3.0 32.0 + - - +
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Residues in contact with TRP 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B TRP* 4.5 10.7 - + + -
385B GLU* 3.1 44.4 - - + +
386B LEU* 4.9 1.6 - - + -
503B ASN 3.7 21.5 - - - -
504B SER 3.8 20.4 - - - -
505B GLY* 4.4 10.8 - - - -
649B LEU 4.5 1.0 + - - -
652B ASN 3.4 0.4 - - - -
653B GLY* 1.3 75.2 - - - +
655B ASP* 1.3 59.5 + - - +
657B LEU* 3.3 18.4 + - + +
658B LYS* 2.9 56.8 + - + +
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Residues in contact with ASP 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B SER 5.1 3.6 - - - +
652B ASN* 2.8 14.0 + - - +
654B TRP* 1.3 79.5 - - - +
656B ARG* 1.3 83.8 + - - +
658B LYS* 3.4 25.3 - - - +
659B ARG* 4.5 22.2 + - - +
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Residues in contact with ARG 656 (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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621B LEU* 4.5 6.7 - - + -
624B ASN* 3.5 28.4 + - - +
628B GLU* 2.6 35.4 + - - +
648B TRP* 3.3 24.5 - - + -
652B ASN* 2.9 56.3 + - - +
653B GLY 3.2 6.4 + - - +
655B ASP* 1.3 103.5 + - - +
657B LEU* 1.3 57.6 + - - +
658B LYS 3.1 4.6 + - - -
659B ARG* 3.2 20.2 + - - +
660B MET* 4.2 7.0 - - - +
672B ILE* 6.0 3.6 - - - +
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Residues in contact with LEU 657 (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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381B TRP* 5.4 2.9 - - + -
382B LEU* 5.0 11.2 - - + -
504B SER 3.4 26.0 - - - +
505B GLY* 2.8 32.7 - - - +
506B GLY* 4.0 6.5 - - - +
617B LEU* 5.1 13.0 - - + -
621B LEU* 3.7 33.8 - - + +
653B GLY 3.0 25.0 + - - +
654B TRP* 3.3 21.7 + - + +
656B ARG* 1.3 73.4 - - - +
658B LYS* 1.3 61.7 + - - +
659B ARG 3.0 1.9 + - - +
660B MET* 4.1 23.5 + - + +
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Residues in contact with LYS 658 (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 ARG* 4.6 11.8 + - - -
505B GLY* 4.3 7.2 - - - +
523B MET* 5.2 2.8 - - - +
654B TRP* 2.9 47.6 + - + +
655B ASP* 3.4 25.4 - - - +
656B ARG 3.1 0.6 - - - -
657B LEU* 1.3 77.2 - - - +
659B ARG* 1.3 64.7 + - + +
660B MET 3.7 1.9 + - - -
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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