Contacts of the helix formed by residues 711 - 719 (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 GLY 711 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669B HIS* 3.4 31.0 - - - -
705B ASP* 3.5 5.6 + - - -
710B HIS* 1.3 71.5 - - - +
712B ASN* 1.3 63.7 + - - -
713B GLY 3.2 2.7 - - - -
714B THR* 3.1 3.3 + - - -
715B GLN* 3.0 22.2 + - - +
726B TYR* 3.2 24.7 + - - -
728B SER* 4.3 0.2 + - - -
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Residues in contact with ASN 712 (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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670B HIS* 2.9 48.6 + - - +
672B ASP* 4.3 11.1 + - - +
677B MET* 3.6 19.3 - - - +
710B HIS* 3.0 16.2 + - - -
711B GLY* 1.3 71.4 - - - +
713B GLY* 1.3 65.5 + - - +
715B GLN* 4.0 1.1 - - - +
716B GLN* 3.1 25.6 + - - +
739B PRO* 3.5 13.6 - - + +
741B SER* 3.4 23.3 - - - +
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Residues in contact with GLY 713 (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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669B HIS 3.0 9.7 + - - -
671B ALA 3.3 25.1 - - - -
672B ASP* 3.9 12.7 - - - -
683B ASN* 3.4 6.5 - - - -
712B ASN* 1.3 81.2 - - - +
714B THR* 1.3 61.7 + - - +
716B GLN* 3.3 4.7 + - - +
717B THR* 2.9 28.3 + - - -
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Residues in contact with THR 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B HIS* 3.7 16.7 + - - +
683B ASN* 3.1 23.6 + - - +
685B VAL* 5.4 2.2 - - + +
686B ALA* 5.0 3.1 - - + +
703B ILE* 3.6 28.5 - - + -
711B GLY 3.1 7.2 + - - -
713B GLY* 1.3 74.1 - - - +
715B GLN* 1.3 62.9 + - - +
717B THR* 3.3 12.1 + - - -
718B PHE* 3.3 28.3 + - + +
726B TYR* 3.5 34.2 - - + -
797B SER* 4.8 3.5 + - - -
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Residues in contact with GLN 715 (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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710B HIS* 2.8 37.5 + - + +
711B GLY 3.0 14.3 + - - +
712B ASN 4.0 2.7 - - - +
714B THR* 1.3 76.2 - - - +
716B GLN* 1.3 64.5 + - - +
718B PHE* 3.5 1.1 + - - -
719B TYR* 3.0 44.1 + - + +
726B TYR* 4.0 8.8 - - + -
741B SER* 5.4 1.4 - - - -
742B GLY 4.6 0.2 - - - +
746B GLU* 2.7 28.9 + - - +
756B ASN* 3.1 29.7 + - - +
758B ASN* 2.9 17.0 + - - +
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Residues in contact with GLN 716 (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 ASP* 3.3 20.9 + - + +
673B HIS* 3.1 38.6 + - - +
712B ASN 3.1 20.2 + - - +
713B GLY* 3.6 3.2 - - - +
714B THR 3.2 0.2 - - - -
715B GLN* 1.3 79.6 - - - +
717B THR* 1.3 67.5 + - - +
718B PHE 3.3 0.5 + - - -
719B TYR* 3.5 15.7 + - - +
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Residues in contact with THR 717 (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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557A GLU* 4.0 10.6 - - - +
580B VAL* 3.9 34.2 + - + +
672B ASP* 5.5 0.5 - - - -
673B HIS* 5.3 2.8 + - - -
683B ASN* 4.8 0.3 + - - -
686B ALA* 4.4 3.4 - - - +
690B ARG* 3.5 35.1 + - - +
713B GLY 2.9 19.0 + - - -
714B THR 3.3 4.7 + - - -
716B GLN* 1.3 83.8 + - - +
718B PHE* 1.3 81.1 + - + +
719B TYR 3.8 0.3 + - - -
720B GLN 5.2 0.2 + - - -
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Residues in contact with PHE 718 (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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202B K 2.5 34.6 - - - -
686B ALA* 3.7 34.3 - - + -
689B CYS* 3.6 18.4 - - - -
690B ARG* 3.8 28.3 - - + -
693B GLN* 4.6 0.9 - - - -
703B ILE* 3.6 22.2 - - + -
714B THR* 3.3 25.2 + - + +
715B GLN* 3.8 1.8 - - - -
716B GLN 3.3 0.4 - - - -
717B THR* 1.3 85.3 - - + +
719B TYR* 1.3 60.9 + - - +
720B GLN 3.1 4.5 + - - -
721B ASP* 3.1 20.8 + - + +
724B VAL* 3.5 40.2 - - + -
726B TYR* 5.5 6.1 - - + -
756B ASN* 5.8 1.1 - - - -
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Residues in contact with TYR 719 (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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202B K 4.7 0.7 - - - -
715B GLN* 3.0 48.4 + - + +
716B GLN* 3.5 14.0 + - - +
717B THR 3.5 0.8 + - - -
718B PHE* 1.3 77.4 - - - +
720B GLN* 1.3 63.1 + - + +
721B ASP 3.5 0.2 - - - -
746B GLU* 3.5 23.9 - - + +
747B VAL* 3.7 0.7 + - - +
748B GLY* 3.3 48.4 + - - -
749B ALA* 3.1 39.3 + - + +
752B GLY* 3.8 5.5 - - - +
756B ASN* 4.1 11.3 - - - +
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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