Contacts of the helix formed by residues 637 - 649 (chain A) in PDB entry 3ZW3
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 ASP 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A HIS* 3.8 9.1 + - + -
425A LYS* 5.1 4.3 - - - +
598A TRP* 3.5 40.9 - - + -
604A VAL* 4.8 2.1 - - - +
608A TYR* 2.6 28.5 + - - -
635A PHE* 3.6 2.0 - - - +
636A SER* 1.3 76.9 - - - +
638A GLU* 1.3 64.8 + - - +
639A ASN* 3.0 26.3 + - - +
640A VAL* 3.1 21.8 + - + +
641A ARG* 3.1 26.6 + - - +
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Residues in contact with GLU 638 (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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425A LYS* 4.3 29.1 + - + +
473A PHE* 4.7 12.3 - - - -
608A TYR* 5.0 3.9 + - - +
636A SER 3.6 4.4 + - - -
637A ASP* 1.3 72.8 + - - +
639A ASN* 1.3 76.0 + - - +
641A ARG* 3.4 6.8 + - - +
642A ALA* 2.9 34.9 + - + +
671A PRO* 6.3 2.0 - - + -
672A TYR* 5.9 5.3 - - + -
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Residues in contact with ASN 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A TYR* 3.3 42.7 + - + -
611A LEU* 4.8 11.9 - - + +
614A ARG* 5.9 0.7 + - - -
637A ASP* 3.0 12.4 + - - +
638A GLU* 1.3 95.7 + - - +
640A VAL* 1.3 63.8 + - - +
642A ALA* 3.5 5.4 + - - +
643A ILE* 3.2 31.0 + - + +
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Residues in contact with VAL 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A PHE* 4.0 26.5 - - + -
598A TRP* 3.8 23.1 - - + -
607A THR* 5.1 0.2 - - + -
611A LEU* 4.2 12.6 - - + -
630A LEU* 4.1 27.6 - - + +
635A PHE* 4.1 23.8 - - + -
637A ASP* 3.1 22.0 + - + +
639A ASN* 1.3 74.6 - - - +
641A ARG* 1.4 64.2 + - - +
643A ILE* 3.1 26.7 - - + +
644A ALA* 3.5 5.9 + - - +
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Residues in contact with ARG 641 (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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630A LEU 3.6 16.7 + - - +
631A LEU* 2.9 38.9 + - + +
632A ASP 3.0 20.0 + - - -
635A PHE* 2.9 33.0 + - + +
636A SER* 4.4 7.4 - - - +
637A ASP 3.1 19.2 + - - +
638A GLU* 3.9 4.9 - - - +
640A VAL* 1.4 74.6 - - - +
642A ALA* 1.3 60.9 - - - +
644A ALA* 3.1 7.8 + - - +
645A VAL* 3.1 25.7 + - + +
666A ALA 3.8 9.9 + - - -
669A PHE* 3.8 13.1 + - - +
670A GLU* 2.8 51.9 + - - +
671A PRO* 4.5 4.9 - - - -
676A ALA* 5.6 0.7 - - - -
677A LEU* 4.5 1.2 - - - +
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Residues in contact with ALA 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLU* 2.9 22.9 + - + +
639A ASN* 3.7 7.6 - - - +
640A VAL 3.3 0.2 - - - -
641A ARG* 1.3 75.5 - - - +
643A ILE* 1.4 58.1 + - + +
645A VAL* 3.2 3.1 + - - +
646A GLN* 2.9 27.5 + - - +
676A ALA* 4.4 21.2 - - + +
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Residues in contact with ILE 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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589A TYR* 4.1 15.7 - - + -
593A PHE* 4.6 5.4 - - + -
611A LEU* 3.9 28.9 - - + -
614A ARG* 3.5 35.7 - - - +
617A TRP* 3.2 44.4 + - + +
630A LEU* 4.6 7.4 - - + -
639A ASN* 3.2 15.5 + - + +
640A VAL* 3.1 20.4 - - - +
642A ALA* 1.4 73.7 - - + +
644A ALA* 1.3 63.6 + - - +
646A GLN* 3.4 20.9 - - - +
647A LYS 3.4 4.2 + - - -
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Residues in contact with ALA 644 (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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617A TRP* 4.4 7.6 - - - -
627A THR* 3.0 50.1 - - + +
630A LEU* 3.7 21.5 - - + -
631A LEU* 3.8 10.5 - - + -
641A ARG 3.1 12.9 + - - +
643A ILE* 1.3 81.7 - - - +
645A VAL* 1.3 61.4 + - - +
647A LYS* 3.2 9.7 + - - +
648A LEU* 3.3 3.9 + - - +
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Residues in contact with VAL 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A LEU* 3.9 17.9 - - + -
641A ARG 3.1 14.7 + - - +
642A ALA 3.2 5.8 + - - +
644A ALA* 1.3 74.4 - - - +
646A GLN* 1.3 63.7 + - - +
648A LEU* 3.0 20.4 + - + +
649A GLU* 3.3 20.6 + - - +
670A GLU* 5.5 0.9 - - - +
676A ALA* 3.7 31.2 - - + +
677A LEU* 3.8 28.0 - - + +
680A PHE* 3.8 21.3 - - + -
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Residues in contact with GLN 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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614A ARG* 3.1 34.9 - - - +
617A TRP* 4.0 7.2 + - - -
618A ASP* 2.8 31.7 + - - +
642A ALA 2.9 13.4 + - - +
643A ILE* 3.4 20.2 + - - +
645A VAL* 1.3 74.1 - - - +
647A LYS* 1.3 66.4 + - - +
649A GLU* 3.3 27.2 - - - +
650A SER* 4.5 1.2 + - - -
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Residues in contact with LYS 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A TRP* 2.7 52.5 + - + +
618A ASP* 2.7 25.1 + - - +
620A SER* 3.0 25.2 + - - -
621A ALA 4.8 0.2 - - - -
622A LEU* 3.5 36.7 - - + +
623A ASP 5.2 0.4 - - - +
627A THR* 4.0 15.0 - - - +
643A ILE 3.4 6.0 + - - +
644A ALA 3.2 10.5 + - - +
645A VAL 3.2 0.4 - - - -
646A GLN* 1.3 81.7 + - - +
648A LEU* 1.3 63.8 + - - +
649A GLU 3.3 0.5 + - - -
650A SER* 3.2 23.1 + - - -
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Residues in contact with LEU 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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622A LEU* 4.7 4.9 - - + -
624A VAL* 5.0 11.2 - - + -
627A THR* 3.6 20.4 - - + -
628A MET* 5.2 2.7 - - - -
631A LEU* 4.0 15.9 - - + -
644A ALA 3.3 10.5 + - - +
645A VAL* 3.0 16.4 + - + +
647A LYS* 1.3 72.9 - - - +
649A GLU* 1.3 64.4 + - - +
650A SER 3.1 3.1 - - - -
651A LEU* 3.0 43.9 + - + +
663A LEU* 3.8 30.3 - - + -
677A LEU* 4.6 4.9 - - + -
680A PHE* 3.6 32.5 - - + -
684A ARG* 4.2 0.2 + - - -
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Residues in contact with GLU 649 (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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645A VAL* 3.3 17.3 + - - +
646A GLN* 3.3 23.3 - - - +
647A LYS 3.2 0.6 - - - -
648A LEU* 1.3 76.3 - - - +
650A SER* 1.3 57.9 + - - +
651A LEU 3.6 1.0 + - - +
680A PHE* 3.5 26.4 - - - +
683A LYS* 3.2 28.6 + - - -
684A ARG* 3.6 13.9 + - - -
687A ARG* 5.2 4.5 + - - -
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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