Contacts of the helix formed by residues 683 - 695 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A VAL* 4.6 1.8 - - + -
581A HIS* 3.1 17.0 + - + +
668A GLY 3.3 16.9 + - - +
669A HIS* 3.7 10.6 + - - +
671A ALA* 3.6 14.1 + - - +
682A PHE* 1.3 68.0 - - - +
684A SER* 1.3 53.8 + - - +
685A VAL* 3.6 7.3 + - - +
686A ALA* 3.0 25.8 + - + +
687A ILE* 2.8 35.3 + - - +
713A GLY 3.5 6.5 - - - -
714A THR* 2.9 45.4 + - - +
717A THR* 4.9 0.2 + - - -
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Residues in contact with SER 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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638A ALA 4.6 0.9 + - - -
641A ALA* 3.4 18.0 - - - +
642A ALA* 3.2 39.8 + - - +
645A VAL* 3.9 15.8 - - - +
646A THR* 4.5 1.6 + - - -
664A VAL* 5.5 2.0 - - - +
666A PRO 4.9 2.4 + - - -
668A GLY* 4.2 8.6 - - - -
682A PHE 3.0 11.6 + - - -
683A ASN* 1.3 71.0 + - - +
685A VAL* 1.3 59.1 + - - +
687A ILE* 3.4 2.2 + - - +
688A ALA* 2.9 30.5 + - - +
838A ALA* 5.9 0.7 - - - -
840A GLU* 5.9 0.7 - - - -
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Residues in contact with VAL 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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645A VAL* 4.4 4.5 - - + -
683A ASN* 3.3 6.8 + - - +
684A SER* 1.3 77.0 - - - +
686A ALA* 1.3 58.0 + - - +
688A ALA* 3.4 5.9 + - - +
689A CYS* 2.9 27.2 + - - +
703A ILE* 4.0 24.7 - - + -
714A THR* 5.3 2.9 - - + +
795A LEU* 3.7 29.0 - - + +
796A VAL 4.5 1.6 - - - +
797A SER* 3.4 27.6 - - - +
838A ALA* 4.0 24.5 - - + -
840A GLU* 3.6 11.6 + - - +
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Residues in contact with ALA 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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580A VAL* 3.6 19.0 - - + +
683A ASN* 3.0 37.6 + - + +
685A VAL* 1.3 74.1 - - - +
687A ILE* 1.3 60.1 + - - +
689A CYS 3.4 0.9 + - - -
690A ARG* 3.0 28.9 + - - +
703A ILE* 5.2 0.2 - - - -
714A THR* 4.9 2.0 + - - +
717A THR* 4.3 5.2 - - - +
718A PHE* 3.6 30.2 - - + -
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Residues in contact with ILE 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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572A ALA* 5.4 1.1 - - + -
576A GLU* 3.5 33.0 - - + +
577A LEU* 3.4 36.8 - - + -
579A SER* 4.6 0.9 - - - -
580A VAL* 3.8 23.8 - - + -
581A HIS* 4.0 6.7 - - + -
642A ALA* 3.9 17.9 - - + +
646A THR* 3.9 11.2 - - - +
682A PHE* 4.0 13.7 - - + -
683A ASN 2.8 17.2 + - - +
684A SER* 3.8 4.9 - - - +
686A ALA* 1.3 73.8 - - - +
688A ALA* 1.3 65.8 + - - +
690A ARG* 3.5 1.9 + - - +
691A GLN* 3.1 25.0 + - + +
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Residues in contact with ALA 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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645A VAL* 3.8 17.5 - - + +
646A THR* 3.3 32.9 + - - +
649A ALA* 4.4 8.5 - - + +
650A PHE* 4.8 0.7 - - - -
684A SER 2.9 18.3 + - - +
685A VAL* 3.6 4.7 - - - +
686A ALA 3.3 0.2 - - - -
687A ILE* 1.3 76.3 - - - +
689A CYS* 1.3 61.9 + - - +
691A GLN* 3.3 2.9 + - - +
692A LEU* 3.1 29.3 + - - +
795A LEU* 4.5 4.3 - - + -
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Residues in contact with CYS 689 (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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685A VAL 2.9 18.1 + - - +
686A ALA 3.6 4.5 - - - +
687A ILE 3.3 0.2 - - - -
688A ALA* 1.3 77.0 - - - +
690A ARG* 1.3 62.7 + - - +
692A LEU* 3.4 1.0 + - - -
693A GLN* 3.2 22.6 + - - +
701A ILE* 3.5 34.1 - - - +
703A ILE* 4.1 7.9 - - + -
718A PHE* 3.7 22.7 - - + -
724A VAL* 3.7 21.1 - - - -
795A LEU* 3.7 15.3 - - + +
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Residues in contact with ARG 690 (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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579A SER* 3.2 41.4 + - - +
580A VAL* 3.6 12.1 + - + +
686A ALA 3.0 19.8 + - - +
687A ILE 3.8 0.9 - - - +
689A CYS* 1.3 75.1 - - - +
691A GLN* 1.3 58.5 + - - +
693A GLN* 3.4 16.6 + - - +
694A GLN* 3.0 51.0 + - - +
717A THR* 3.0 46.8 + - - +
718A PHE* 3.7 19.9 - - + +
721A ASP* 4.7 9.9 + - - +
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Residues in contact with GLN 691 (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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575A GLU 4.7 0.3 - - - +
576A GLU* 3.8 37.0 + - + +
579A SER* 3.2 27.7 + - - -
646A THR* 4.2 10.1 - - + -
650A PHE* 3.6 20.8 - - + -
687A ILE* 3.1 22.0 + - + +
688A ALA 3.7 2.2 - - - +
690A ARG* 1.3 75.0 - - - +
692A LEU* 1.3 60.2 + - - +
694A GLN* 3.9 12.3 + - - +
695A GLN* 2.8 49.8 + - - +
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Residues in contact with LEU 692 (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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649A ALA* 3.5 26.5 - - + +
650A PHE* 3.3 53.2 - - + +
653A ALA* 4.1 14.1 - - + -
688A ALA 3.1 18.1 + - - +
689A CYS* 3.6 7.9 - - - +
691A GLN* 1.3 75.6 - - - +
693A GLN* 1.3 55.9 + - - +
696A SER 3.3 1.7 + - - -
697A LYS* 2.7 34.6 + - + +
698A ALA* 3.4 12.3 + - + -
701A ILE* 3.9 14.4 - - + -
793A LEU* 4.2 23.1 - - + -
795A LEU* 4.7 2.2 - - + -
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Residues in contact with GLN 693 (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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689A CYS* 3.2 13.4 + - - +
690A ARG* 3.6 25.9 + - - +
691A GLN 3.2 0.8 - - - -
692A LEU* 1.3 75.2 - - - +
694A GLN* 1.3 63.7 + - + +
696A SER* 3.0 20.1 + - - -
698A ALA 4.0 13.0 - - - +
699A SER 4.2 4.2 + - - +
701A ILE* 3.9 12.7 - - + +
718A PHE* 4.6 0.9 - - - -
721A ASP* 3.5 11.0 + - - +
723A SER* 2.7 34.6 + - - -
724A VAL* 3.3 24.2 - - - +
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Residues in contact with GLN 694 (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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579A SER* 4.0 24.4 + - - +
690A ARG* 3.0 35.6 + - - +
691A GLN* 3.9 19.4 + - - +
693A GLN* 1.3 78.6 - - + +
695A GLN* 1.3 65.3 + - - +
696A SER* 3.2 5.7 + - - -
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Residues in contact with GLN 695 (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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650A PHE* 3.5 31.0 - - + -
691A GLN* 2.8 31.3 + - - +
692A LEU 4.4 0.9 - - - +
694A GLN* 1.3 79.4 - - - +
696A SER* 1.3 70.7 + - - +
697A LYS* 3.1 8.3 + - + +
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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