Contacts of the helix formed by residues 683 - 696 (chain B) in PDB entry 3ZNS
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 ASN 683 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580B VAL* 4.5 3.4 - - + -
581B HIS* 3.0 16.6 + - + +
668B GLY 3.3 23.2 + - - +
669B HIS* 3.9 2.4 + - - +
671B ALA* 3.5 15.2 + - - +
682B PHE* 1.3 67.7 - - - +
684B SER* 1.3 58.6 + - - +
685B VAL* 3.7 6.1 + - - +
686B ALA* 3.1 24.3 + - + +
687B ILE* 2.9 32.5 + - - +
713B GLY* 3.4 8.1 + - - -
714B THR* 3.1 45.5 + - - +
717B THR* 4.8 0.6 + - - -
840B GLU* 5.0 0.2 - - - +
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Residues in contact with SER 684 (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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638B ALA 4.8 0.9 + - - -
641B ALA* 3.7 15.4 - - - +
642B ALA* 3.4 41.6 + - - +
645B VAL* 4.1 16.6 - - - +
664B VAL* 5.8 1.8 - - - -
666B PRO 4.8 2.9 + - - -
668B GLY* 4.2 9.2 + - - -
682B PHE 3.1 12.1 + - - -
683B ASN* 1.3 72.0 + - - +
685B VAL* 1.3 60.2 + - - +
687B ILE* 3.4 2.6 + - - +
688B ALA* 3.0 28.8 + - - +
838B ALA* 6.0 0.2 - - - -
840B GLU* 5.9 0.2 - - - -
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Residues in contact with VAL 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B VAL* 4.5 4.3 - - + -
683B ASN* 3.3 7.2 + - - +
684B SER* 1.3 75.2 - - - +
686B ALA* 1.3 61.4 + - - +
688B ALA* 3.4 5.1 + - - +
689B CYS* 3.0 23.6 + - - +
703B ILE* 4.0 23.1 - - + -
714B THR* 5.4 2.2 - - + +
795B LEU* 3.4 37.4 - - + +
796B VAL 4.4 4.3 - - - +
797B SER* 3.7 11.0 - - - +
838B ALA* 3.7 27.1 - - + -
840B GLU* 3.5 21.5 + - - +
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Residues in contact with ALA 686 (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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580B VAL* 3.7 16.8 - - + -
683B ASN* 3.1 33.5 + - + +
685B VAL* 1.3 75.5 - - - +
687B ILE* 1.3 61.9 + - - +
689B CYS* 3.3 2.8 + - - +
690B ARG* 3.0 32.7 + - - +
703B ILE* 4.9 0.9 - - - -
714B THR* 5.0 2.8 + - + -
717B THR* 4.4 4.0 - - - +
718B PHE* 3.7 27.7 - - + -
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Residues in contact with ILE 687 (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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572B ALA* 5.3 1.3 - - + -
576B GLU* 3.7 27.6 - - + +
577B LEU* 3.5 34.5 - - + +
579B SER* 4.6 0.4 - - - -
580B VAL* 3.8 22.9 - - + -
581B HIS* 4.2 6.7 - - + -
642B ALA* 4.0 16.8 - - + -
646B THR* 3.8 13.9 - - - +
682B PHE* 4.0 11.4 - - + -
683B ASN 2.9 21.1 + - - +
684B SER* 3.7 4.9 - - - +
685B VAL 3.3 0.2 - - - -
686B ALA* 1.3 75.7 - - - +
688B ALA* 1.3 62.8 + - - +
690B ARG* 3.3 3.1 + - - +
691B GLN* 3.0 29.2 + - + +
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Residues in contact with ALA 688 (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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645B VAL* 3.9 16.8 - - + +
646B THR* 3.5 31.2 + - - +
649B ALA* 4.3 9.9 - - + -
684B SER 3.0 18.0 + - - +
685B VAL 3.6 4.7 - - - +
686B ALA 3.3 0.2 - - - -
687B ILE* 1.3 75.5 - - - +
689B CYS* 1.3 57.4 + - - +
691B GLN* 3.3 1.7 + - - -
692B LEU* 2.9 37.8 + - - +
795B LEU* 4.3 7.2 - - + -
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Residues in contact with CYS 689 (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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685B VAL 3.0 13.9 + - - +
686B ALA* 3.4 9.4 - - - +
688B ALA* 1.3 76.5 - - - +
690B ARG* 1.3 61.8 + - - +
692B LEU* 3.5 2.5 + - - +
693B GLN* 3.1 30.6 + - - +
701B ILE* 3.8 25.7 - - - +
703B ILE* 4.3 3.8 - - + -
718B PHE* 3.6 16.4 - - + -
724B VAL* 3.5 35.7 - - - -
795B LEU* 3.5 14.7 - - + +
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Residues in contact with ARG 690 (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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556A GLN* 3.2 45.6 + - - +
557A GLU* 3.6 16.0 + - - +
559A GLY* 5.6 1.2 - - - -
562A SER* 5.3 1.0 - - - -
579B SER* 3.1 43.0 + - - +
580B VAL* 4.0 5.7 - - + +
686B ALA 3.0 19.0 + - - +
687B ILE 3.3 4.5 + - - +
689B CYS* 1.3 74.9 - - - +
691B GLN* 1.3 63.8 + - - +
693B GLN* 3.3 13.1 + - - +
694B GLN* 3.2 27.7 + - - +
717B THR* 3.5 28.7 + - - +
718B PHE* 3.8 18.4 - - + -
721B ASP* 3.4 19.4 + - - -
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Residues in contact with GLN 691 (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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575B GLU 4.8 0.3 - - - +
576B GLU* 3.7 40.9 + - + +
579B SER* 3.3 26.5 + - - -
646B THR* 4.2 7.2 - - + -
650B PHE* 3.6 23.3 - - + -
687B ILE* 3.0 25.5 + - + +
688B ALA 3.8 2.0 - - - +
690B ARG* 1.3 71.9 - - - +
692B LEU* 1.3 68.2 + - - +
694B GLN* 3.2 26.5 + - - +
695B GLN* 2.9 32.6 + - - +
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Residues in contact with LEU 692 (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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646B THR 4.4 0.2 - - - +
649B ALA* 3.6 28.9 - - + -
650B PHE* 3.3 37.0 - - + +
653B ALA* 4.3 13.5 - - + -
688B ALA 2.9 24.8 + - - +
689B CYS 3.6 4.7 - - - +
691B GLN* 1.3 76.2 - - - +
693B GLN* 1.3 57.3 - - - +
695B GLN* 3.3 3.8 + - - +
696B SER* 3.1 31.9 + - - -
699B SER* 4.4 1.3 + - - -
701B ILE* 3.8 17.5 - - + -
793B LEU* 3.8 32.5 - - + -
795B LEU* 4.6 2.5 - - + -
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Residues in contact with GLN 693 (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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559A GLY* 5.8 1.3 - - - -
562A SER* 3.4 29.2 + - - +
689B CYS* 3.1 25.8 + - - +
690B ARG* 3.7 16.4 + - - +
691B GLN 3.1 0.2 - - - -
692B LEU* 1.3 75.2 - - - +
694B GLN* 1.3 62.2 + - - +
696B SER 3.1 17.5 - - - +
697B LYS* 4.3 0.2 - - - -
698B ALA 5.1 0.5 + - - -
699B SER* 3.1 35.7 + - - +
701B ILE* 4.0 10.8 - - + +
721B ASP* 4.3 5.0 - - - +
723B SER* 3.0 30.2 + - - -
724B VAL* 3.4 26.7 - - - +
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Residues in contact with GLN 694 (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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556A GLN* 4.2 10.1 - - - +
561A ARG* 5.2 6.2 - - - +
562A SER* 3.9 23.8 - - - +
575B GLU* 5.0 7.1 - - - +
579B SER* 4.1 15.2 - - - -
690B ARG* 3.2 15.6 + - - +
691B GLN* 3.2 35.2 + - - +
693B GLN* 1.3 76.2 - - - +
695B GLN* 1.3 69.9 + - - +
696B SER* 3.4 1.6 + - - -
697B LYS* 4.5 12.0 + - - +
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Residues in contact with GLN 695 (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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650B PHE* 3.4 32.6 - - + -
691B GLN* 2.9 37.5 + - - +
692B LEU* 3.9 4.3 - - - +
694B GLN* 1.3 85.4 + - - +
696B SER* 1.3 62.9 + - - +
697B LYS* 4.2 1.3 - - - -
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Residues in contact with SER 696 (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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653B ALA* 5.7 4.9 - - - +
692B LEU 3.1 12.6 + - - -
693B GLN 3.1 11.3 - - - +
694B GLN 3.2 1.2 - - - -
695B GLN* 1.3 85.3 + - - +
697B LYS* 1.3 63.8 + - - +
698B ALA 3.5 0.2 + - - -
699B SER* 3.0 31.1 + - - -
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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