Contacts of the helix formed by residues 675 - 688 (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 SER 675 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667A VAL* 5.5 1.0 - - - +
670A GLU* 3.3 42.2 - - - +
672A TYR* 4.1 7.2 + - - -
673A HIS 3.6 1.6 + - - -
674A ASP* 1.3 76.2 + - - +
676A ALA* 1.4 65.1 + - - +
677A LEU 3.6 0.5 + - - -
678A ALA* 3.0 25.3 + - - +
679A ARG* 3.0 28.0 + - - +
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Residues in contact with ALA 676 (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 ARG 5.6 0.2 - - - -
642A ALA* 4.4 19.7 - - + +
645A VAL* 3.7 26.3 - - + +
670A GLU* 5.4 0.2 + - - -
675A SER* 1.4 72.7 - - - +
677A LEU* 1.4 56.7 + - - +
679A ARG* 3.4 9.1 + - - +
680A PHE* 2.9 28.8 + - - +
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Residues in contact with LEU 677 (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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631A LEU* 4.7 8.5 - - + -
641A ARG* 4.5 3.6 - - - +
645A VAL* 3.8 20.3 - - + +
648A LEU* 4.6 7.9 - - + -
663A LEU* 3.8 27.6 - - + +
666A ALA* 3.7 42.6 - - + +
667A VAL* 3.9 12.3 - - + +
670A GLU* 3.6 23.2 + - - +
675A SER* 3.2 3.6 + - - +
676A ALA* 1.4 75.4 - - - +
678A ALA* 1.3 65.5 + - - +
680A PHE* 3.1 10.0 + - + +
681A LEU* 3.1 34.3 + - + +
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Residues in contact with ALA 678 (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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180A LEU* 5.3 6.5 - - + -
667A VAL* 4.7 6.2 - - + +
673A HIS 4.0 13.9 - - - +
674A ASP* 5.1 0.7 - - - -
675A SER* 3.0 22.8 + - - +
677A LEU* 1.3 77.5 - - - +
679A ARG* 1.3 63.3 + - + +
681A LEU* 3.5 10.2 + - - +
682A LEU* 3.1 23.6 + - - +
716A ILE* 3.8 34.7 - - + +
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Residues in contact with ARG 679 (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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179A GLY* 3.3 20.5 + - - -
180A LEU* 3.9 12.4 - - + +
182A THR* 5.7 3.4 - - - +
183A PRO* 4.0 27.6 - - + +
674A ASP* 2.9 37.8 + - - +
675A SER 3.0 20.2 + - - +
676A ALA* 3.7 7.6 - - - +
678A ALA* 1.3 72.3 - - - +
680A PHE* 1.3 64.8 + - - +
682A LEU* 3.4 8.0 + - - +
683A LYS* 3.0 33.5 + - + +
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Residues in contact with PHE 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A VAL* 3.8 15.9 - - + -
648A LEU* 3.6 48.5 - - + -
649A GLU* 3.5 25.8 - - - +
651A LEU* 4.6 1.3 - - + -
656A VAL* 4.4 11.9 - - + -
663A LEU* 4.1 21.5 - - + -
676A ALA 2.9 14.1 + - - +
677A LEU* 3.1 11.9 + - + +
679A ARG* 1.3 75.4 - - - +
681A LEU* 1.3 75.7 + - + +
683A LYS* 3.3 12.2 + - - +
684A ARG* 3.1 60.8 + - + +
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Residues in contact with LEU 681 (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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656A VAL* 5.9 1.1 - - + -
660A LEU* 3.9 28.3 - - + +
663A LEU* 3.8 31.9 - - + +
664A VAL* 4.0 14.4 - - + +
667A VAL* 3.7 31.2 - - + -
677A LEU* 3.1 16.8 + - + +
678A ALA* 3.8 7.2 - - - +
680A PHE* 1.3 85.0 - - + +
682A LEU* 1.3 63.2 + - - +
684A ARG* 3.4 3.9 + - + +
685A GLY 3.0 19.6 + - - -
691A ILE* 5.2 1.0 - - - +
695A LEU* 3.7 21.6 - - + +
699A LEU* 6.1 1.6 - - + -
716A ILE* 5.5 5.4 - - + -
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Residues in contact with LEU 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.0 36.3 - - + +
183A PRO* 4.5 7.9 - - + -
184A ARG* 4.3 12.6 - - + +
678A ALA 3.1 17.4 + - - +
679A ARG* 3.6 4.5 - - - +
681A LEU* 1.3 75.2 - - - +
683A LYS* 1.3 57.1 + - + +
685A GLY* 3.8 0.9 - - - -
686A LEU* 3.0 47.6 + - + +
695A LEU* 4.6 6.7 - - - +
716A ILE* 4.5 10.2 - - + +
719A ALA* 3.6 17.0 - - + +
720A TYR* 3.4 41.1 - - + +
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Residues in contact with LYS 683 (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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183A PRO* 4.5 20.6 - - + +
187A GLU* 3.4 36.6 - - + +
649A GLU* 3.2 33.0 + - - -
679A ARG* 3.0 24.8 + - + +
680A PHE* 3.7 12.7 - - - +
682A LEU* 1.3 78.4 - - + +
684A ARG* 1.3 60.0 + - - +
686A LEU 3.4 0.9 + - - -
687A ARG* 3.0 47.8 + - - +
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Residues in contact with ARG 684 (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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648A LEU 4.2 0.6 + - - -
649A GLU* 3.6 16.9 + - - -
651A LEU 2.9 29.5 + - - -
652A GLU* 3.6 2.2 - - - +
653A ASP* 2.9 37.8 + - - +
656A VAL* 3.6 31.4 - - + +
660A LEU* 6.3 0.4 - - + -
680A PHE* 3.1 49.8 + - + +
681A LEU* 4.1 3.8 - - + +
683A LYS* 1.3 77.6 - - - +
685A GLY* 1.3 61.5 + - - +
687A ARG* 3.4 38.2 + - - +
688A ASN* 3.3 19.4 + - - +
691A ILE* 3.6 16.3 - - + +
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Residues in contact with GLY 685 (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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196A TYR* 5.0 0.2 - - - -
681A LEU 3.0 15.8 + - - -
682A LEU 3.8 1.6 - - - -
684A ARG* 1.3 77.8 - - - +
686A LEU* 1.3 57.2 + - - +
688A ASN 2.9 20.3 + - - +
689A LYS* 4.8 0.7 - - - -
691A ILE* 3.7 15.4 - - - +
692A GLY* 3.4 18.2 - - - -
695A LEU* 4.3 5.6 - - - -
720A TYR* 3.4 14.4 + - - -
728A MET* 4.9 1.4 - - - +
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Residues in contact with LEU 686 (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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184A ARG* 3.9 35.4 - - + +
187A GLU* 3.9 17.9 - - + -
188A VAL* 4.7 1.1 - - + -
191A ARG* 3.1 29.6 + - - +
196A TYR* 3.2 13.5 - - - -
682A LEU* 3.0 39.2 + - + +
683A LYS* 4.9 0.2 - - - -
685A GLY* 1.3 76.3 - - - +
687A ARG* 1.3 59.0 + - - +
688A ASN 3.4 0.2 - - - -
720A TYR* 3.4 28.3 - - + +
723A GLY* 3.3 37.5 - - - +
724A CYS* 3.5 2.0 - - - +
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Residues in contact with ARG 687 (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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187A GLU* 3.0 37.5 + - - +
191A ARG* 5.1 8.9 - - + +
196A TYR* 3.9 14.7 - - - +
649A GLU* 5.2 4.0 + - - -
653A ASP* 4.9 8.3 - - - +
683A LYS* 3.0 36.6 + - - +
684A ARG* 3.4 46.1 - - - +
685A GLY 3.3 0.4 - - - -
686A LEU* 1.3 78.8 - - - +
688A ASN* 1.4 60.3 + - + +
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Residues in contact with ASN 688 (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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196A TYR* 4.5 2.5 - - - -
199A HIS* 5.2 10.0 - - - +
200A PRO 4.6 12.7 + - - -
653A ASP* 2.9 34.2 + - - +
657A LEU* 5.5 1.7 - - - +
684A ARG 3.3 10.7 + - - +
685A GLY 2.9 7.3 - - - +
686A LEU 3.4 0.6 - - - -
687A ARG* 1.4 79.5 - - - +
689A LYS* 1.3 59.2 + - - +
690A ARG* 2.9 32.5 + - - +
691A ILE* 2.9 23.7 + - + +
692A GLY 2.9 24.1 + - - -
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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