Contacts of the helix formed by residues 639 - 648 (chain A) in PDB entry 2WKP
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 639 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A ASP* 5.4 0.9 - - - +
603A GLY 5.1 0.6 + - - -
605A GLU* 4.2 17.6 + - - +
608A ASP* 2.7 33.7 + - - -
611A ARG* 4.2 0.2 - - - +
635A HIS* 2.8 20.7 + - + +
637A ARG 3.4 0.4 - - - -
638A ALA* 1.3 81.0 - - + +
640A TRP* 1.3 101.9 + - + +
642A PRO* 3.4 5.3 - - - +
643A GLU* 3.0 56.9 + - + +
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Residues in contact with TRP 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A VAL* 3.9 19.5 - - + -
553A GLY* 3.3 36.8 - - - -
554A ASP* 2.8 30.4 + - - +
601A THR* 6.0 0.2 - - - -
603A GLY* 3.7 15.5 - - - -
611A ARG* 3.5 53.8 - - - -
615A TYR* 5.0 0.4 - - - -
623A ILE* 3.8 27.4 - - + -
624A CYS 5.0 0.9 - - - -
632A SER 4.9 1.6 - - - -
635A HIS* 3.0 34.0 + - + +
636A VAL* 4.1 7.0 - - + +
639A LYS* 1.3 91.7 - - + +
641A TYR* 1.3 66.8 + - - +
643A GLU* 3.3 7.6 + - + +
644A VAL* 2.9 30.8 + - + +
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Residues in contact with TYR 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ILE* 4.0 9.3 - - + +
636A VAL 2.9 15.5 + - - +
637A ARG* 4.5 7.4 - - + -
640A TRP* 1.3 76.3 - - - +
642A PRO* 1.3 75.1 - - + +
644A VAL* 3.9 1.1 - - - +
645A ARG* 2.9 58.1 + - + +
653A ILE* 4.2 9.6 - - + -
691A GLU* 4.8 3.8 + - + -
692A ILE* 3.1 65.1 + - + -
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Residues in contact with PRO 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A ARG 3.2 27.8 - - - +
638A ALA 3.7 14.8 - - - +
639A LYS 3.4 11.7 - - - +
641A TYR* 1.3 98.8 - - + +
643A GLU* 1.3 57.7 + - - +
645A ARG* 3.8 4.7 - - + +
646A HIS* 2.9 30.7 + - - +
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Residues in contact with GLU 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A ASP* 4.1 7.6 - - - +
611A ARG* 2.9 32.3 + - - +
612A PRO* 4.5 6.9 - - - +
615A TYR* 2.6 35.1 + - + +
639A LYS* 3.0 35.5 + - + +
640A TRP* 3.9 8.0 - - + +
642A PRO* 1.3 73.4 - - - +
644A VAL* 1.3 68.8 + - + +
646A HIS* 3.3 9.9 + - - +
647A HIS* 3.2 32.1 - - + +
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Residues in contact with VAL 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A VAL* 4.2 13.5 - - + -
615A TYR* 4.7 13.5 - - - +
621A PHE* 3.6 50.5 - - + -
623A ILE* 4.2 15.5 - - + -
640A TRP* 2.9 20.4 + - + +
641A TYR 3.9 2.2 - - - +
643A GLU* 1.3 77.5 - - + +
645A ARG* 1.3 64.8 + - - +
647A HIS* 3.2 3.1 + - - +
648A CYS* 2.8 27.9 + - - +
653A ILE* 4.1 19.7 - - + -
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Residues in contact with ARG 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A TYR* 2.9 48.6 + - + +
642A PRO* 4.1 4.7 - - + +
644A VAL* 1.3 80.4 - - - +
646A HIS* 1.3 64.4 + - - +
648A CYS 2.8 21.4 + - - -
649A PRO* 3.3 47.4 + - + +
650A ASN 4.8 1.6 - - - -
651A THR 2.8 33.3 + - - +
652A PRO* 4.6 1.2 - - - +
653A ILE* 3.4 28.9 - - + +
692A ILE 5.0 1.6 + - - -
693A GLY 4.6 10.9 + - - -
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Residues in contact with HIS 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A PRO 2.9 18.4 + - - +
643A GLU* 3.5 7.9 - - + +
644A VAL 3.2 0.2 - - - -
645A ARG* 1.3 78.8 - - - +
647A HIS* 1.3 87.0 + + - +
649A PRO* 4.9 4.0 - - - +
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Residues in contact with HIS 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A PRO* 3.6 29.3 + - + +
615A TYR* 3.7 35.4 - + + +
643A GLU* 3.2 27.4 + - + +
644A VAL 3.2 4.7 + - - +
646A HIS* 1.3 99.7 - + - +
648A CYS* 1.3 69.6 + - - +
649A PRO* 3.6 7.7 - - - +
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Residues in contact with CYS 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A TYR* 3.8 20.0 - - - -
616A PRO* 5.5 1.6 - - - -
617A GLN 5.9 0.4 - - - -
618A THR* 5.0 1.3 - - - -
621A PHE* 3.7 32.3 - - + -
644A VAL 2.8 18.2 + - - +
645A ARG* 2.8 25.2 + - - -
647A HIS* 1.3 88.3 - - - +
649A PRO* 1.3 62.8 - - - +
650A ASN 3.1 3.4 + - - -
651A THR* 3.4 20.8 + - - +
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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