Contacts of the helix formed by residues 669 - 681 (chain B) in PDB entry 1WZ2
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 GLY 669 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ASN 5.5 2.7 - - - -
6B PHE* 6.3 1.8 - - - -
7B LYS* 5.0 8.0 - - - +
10B GLU* 3.2 14.4 - - - -
665B ILE 2.6 24.2 + - - -
666B GLU 4.5 1.2 + - - -
668B ASN* 1.3 73.6 - - - +
670B ALA* 1.3 71.1 + - - +
671B ASP 3.5 1.3 - - - -
672B VAL* 3.2 5.3 + - - -
673B VAL* 3.0 20.0 + - - +
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Residues in contact with ALA 670 (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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10B GLU* 2.9 18.5 + - - +
139B ARG 3.9 13.9 - - - +
140B ALA* 4.1 9.2 - - - +
665B ILE* 3.4 15.2 - - + +
669B GLY* 1.3 71.9 - - - +
671B ASP* 1.3 57.5 + - - +
673B VAL* 2.8 3.4 + - - +
674B ARG* 2.7 41.2 + - + -
800B HIS* 3.5 28.5 - - + +
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Residues in contact with ASP 671 (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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6B PHE* 6.4 0.4 - - + -
10B GLU* 4.6 2.3 + - + +
669B GLY 3.5 0.4 - - - -
670B ALA* 1.3 77.7 - - - +
672B VAL* 1.3 68.3 + - + +
674B ARG* 3.9 4.4 - - - +
675B LEU* 3.1 10.9 + - - +
701B ILE* 5.5 1.3 - - + -
798B THR* 2.8 57.9 - - + +
799B PRO* 2.9 24.8 - - - +
800B HIS* 2.9 27.9 + - + -
801B ILE* 2.9 27.1 + - + +
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Residues in contact with VAL 672 (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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6B PHE* 5.4 5.6 - - + -
668B ASN* 3.0 30.1 - - + +
669B GLY* 3.2 2.2 + - - +
670B ALA 2.9 4.6 + - - -
671B ASP* 1.3 77.8 - - + +
673B VAL* 1.3 65.9 + - - +
675B LEU* 3.0 1.7 + - - +
676B TYR* 2.7 22.1 + - - +
694B VAL* 4.1 20.9 - - + +
697B LEU* 4.8 4.9 - - + -
698B ARG* 3.6 45.8 - - + +
701B ILE* 4.4 27.1 - - + +
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Residues in contact with VAL 673 (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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51B VAL* 5.6 1.8 - - + -
661B PHE* 4.4 25.1 - - + -
664B ALA* 3.6 28.9 - - + +
665B ILE* 3.9 11.2 - - + -
668B ASN* 3.7 14.1 - - + -
669B GLY 3.0 13.0 + - - +
670B ALA* 2.8 10.9 + - - +
672B VAL* 1.3 74.6 - - - +
674B ARG* 1.3 69.6 + - + +
676B TYR* 2.9 17.4 + - - +
677B ILE* 3.1 15.5 + - + +
689B TRP* 3.8 25.1 - - + -
694B VAL* 5.4 0.4 - - - -
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Residues in contact with ARG 674 (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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58B THR* 4.5 22.7 - - + +
61B ASP* 2.9 24.9 + - - +
62B VAL* 4.8 4.8 - - - +
65B ARG* 3.5 9.3 - - - +
140B ALA* 2.3 47.9 + - + -
141B GLY 2.7 19.2 + - - -
142B PHE* 3.8 9.9 - - - -
661B PHE* 5.4 5.2 - - + -
670B ALA* 2.7 34.3 + - - +
671B ASP* 3.7 4.3 - - - +
673B VAL* 1.3 77.7 - - + +
675B LEU* 1.3 63.4 + - - +
677B ILE* 3.1 18.2 + - - +
678B MET* 3.5 11.3 + - - +
796B PRO 2.9 25.5 + - - -
797B PHE 3.2 13.7 + - - +
799B PRO* 3.7 12.2 - - - +
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Residues in contact with LEU 675 (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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671B ASP 3.1 12.0 + - - +
672B VAL 3.0 3.1 + - - +
674B ARG* 1.3 80.0 - - - +
676B TYR* 1.3 57.1 + - - +
678B MET* 3.4 4.1 + - - +
679B SER* 2.8 33.8 + - - -
697B LEU* 3.1 41.1 - - + -
701B ILE* 3.6 20.0 - - + -
753B VAL* 4.3 16.2 - - + -
757B PHE* 4.3 13.0 - - + -
758B TYR* 5.6 0.7 - - + -
794B MET* 3.4 36.1 - - + -
797B PHE* 3.8 21.7 + - + -
798B THR* 3.9 8.1 - - + -
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Residues in contact with TYR 676 (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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672B VAL 2.7 16.2 + - - +
673B VAL 2.9 8.0 + - - +
675B LEU* 1.3 73.4 - - - +
677B ILE* 1.3 59.7 + - - +
679B SER* 3.0 17.2 + - - -
680B LEU* 3.4 31.1 + - + +
689B TRP* 3.4 47.3 - + - -
690B ARG 3.0 18.7 + - - -
693B GLU* 2.8 44.1 + - + +
694B VAL* 3.6 31.6 - - + -
697B LEU* 3.2 29.2 - - + -
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Residues in contact with ILE 677 (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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51B VAL* 3.8 6.3 - - + -
54B ALA* 5.0 3.6 - - + -
55B ARG* 3.8 40.1 + - + +
58B THR* 5.2 4.7 - - - +
661B PHE* 6.1 0.2 - - + -
673B VAL* 3.1 19.6 + - + +
674B ARG* 3.3 9.9 - - - +
675B LEU 3.0 1.2 + - - -
676B TYR* 1.3 73.7 - - + +
678B MET* 1.3 71.6 + - - +
679B SER 2.8 3.6 - - - -
680B LEU* 2.7 33.0 + - + +
681B ALA 3.8 3.6 + - - +
687B PHE* 3.7 27.9 - - + -
689B TRP* 3.4 37.2 - - + -
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Residues in contact with MET 678 (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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55B ARG* 5.4 0.2 - - - -
58B THR* 3.4 19.3 - - + -
59B ILE* 3.5 27.1 - - + -
62B VAL* 3.2 30.1 - - + -
674B ARG 3.6 13.5 - - - +
675B LEU 3.4 2.0 + - - +
677B ILE* 1.3 86.8 - - - +
679B SER* 1.3 63.3 + - - +
680B LEU 3.1 0.9 + - - -
681B ALA 3.7 3.4 + - - -
749B THR* 3.2 48.2 + - + -
750B ARG* 3.1 25.6 + - - -
753B VAL* 4.0 15.7 - - + -
797B PHE* 4.2 13.9 - - + -
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Residues in contact with SER 679 (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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675B LEU* 2.8 22.0 + - - -
676B TYR* 3.0 26.0 + - - -
678B MET* 1.3 77.4 - - - +
680B LEU* 1.3 57.5 + - - +
697B LEU* 4.3 5.4 - - - -
750B ARG* 3.0 23.4 - - - +
753B VAL* 3.8 22.8 - - - +
758B TYR* 3.8 18.5 + - - -
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Residues in contact with LEU 680 (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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676B TYR* 3.4 49.1 - - + +
677B ILE* 2.7 17.2 + - - +
679B SER* 1.3 73.8 - - - +
681B ALA* 1.3 61.8 + - - +
687B PHE* 3.9 27.5 - - + +
688B ASP 3.8 17.7 - - - +
693B GLU* 3.4 24.2 - - - +
750B ARG* 3.1 16.0 - - - +
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Residues in contact with ALA 681 (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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55B ARG* 3.4 23.3 + - - +
677B ILE 3.8 3.3 + - - +
678B MET* 3.7 3.4 + - - +
680B LEU* 1.3 80.7 - - - +
682B GLU* 1.3 62.8 + - - +
685B SER* 3.8 10.1 - - - +
686B ASP 3.8 22.2 - - - +
687B PHE* 4.2 8.2 - - + +
749B THR* 2.8 18.2 + - - -
750B ARG* 3.0 15.2 + - - +
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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