Contacts of the helix formed by residues 711 - 718 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669C HIS* 3.2 34.4 + - - -
705C ASP* 3.5 1.0 + - - -
709C HIS 3.5 4.4 + - - -
710C HIS* 1.3 70.8 - - - +
712C ASN* 1.3 66.4 + - - -
713C GLY 3.3 2.5 - - - -
714C THR* 3.1 3.5 + - - -
715C GLN* 3.0 21.1 + - - +
726C TYR* 3.3 23.8 + - - -
728C SER* 4.4 0.4 + - - -
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Residues in contact with ASN 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670C HIS* 2.7 48.3 + - - -
672C ASP* 5.1 5.4 - - - +
677C MET* 3.4 24.0 - - - +
710C HIS* 2.9 17.8 + - - +
711C GLY* 1.3 71.2 - - - -
713C GLY* 1.3 58.5 + - - +
715C GLN* 3.3 2.9 + - - +
716C GLN* 2.9 30.8 + - - +
739C PRO* 3.6 10.6 - - + +
741C SER* 3.5 21.3 - - - +
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Residues in contact with GLY 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C HIS 3.1 8.7 + - - -
670C HIS 3.9 0.6 + - - -
671C ALA 3.5 22.4 - - - -
672C ASP* 4.0 16.3 - - - +
683C ASN* 3.5 6.1 - - - -
712C ASN* 1.3 81.7 - - - +
714C THR* 1.3 52.1 + - - +
716C GLN* 3.3 2.3 + - - +
717C THR* 2.6 38.3 + - - -
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Residues in contact with THR 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C HIS* 3.5 16.7 + - - +
683C ASN* 2.9 26.5 + - - +
685C VAL* 5.2 2.8 - - + +
686C ALA* 5.0 1.3 - - + -
703C ILE* 3.7 27.1 - - + -
711C GLY 3.1 7.3 + - - -
713C GLY* 1.3 73.7 - - - +
715C GLN* 1.3 64.1 + - - +
717C THR* 3.4 7.5 + - - -
718C PHE* 3.4 26.3 + - + +
726C TYR* 3.4 35.0 - - + +
797C SER* 5.0 2.3 + - - -
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Residues in contact with GLN 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710C HIS* 2.8 34.9 + - + +
711C GLY 3.0 12.0 + - - +
712C ASN 3.6 6.5 - - - +
714C THR* 1.3 78.6 - - - +
716C GLN* 1.3 63.8 + - - +
718C PHE 3.9 1.0 - - - -
719C TYR* 3.3 45.1 + - + +
726C TYR* 4.1 7.7 - - + -
741C SER* 5.8 0.6 - - - -
746C GLU* 2.9 26.9 + - - +
756C ASN* 3.3 29.5 + - - +
758C ASN* 2.9 16.6 + - - +
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Residues in contact with GLN 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672C ASP* 3.3 32.1 - - - +
712C ASN 2.9 17.0 + - - +
713C GLY 3.6 1.1 - - - +
715C GLN* 1.3 78.6 - - - +
717C THR* 1.3 64.3 + - - +
719C TYR* 3.6 14.9 + - - +
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Residues in contact with THR 717 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580C VAL* 4.2 32.3 + - + +
672C ASP* 4.6 5.7 + - - -
673C HIS* 5.1 3.9 + - - +
683C ASN* 4.8 0.3 + - - -
686C ALA* 4.4 3.6 - - + +
690C ARG* 3.3 36.3 + - - +
713C GLY 2.6 23.3 + - - -
714C THR* 3.9 4.8 - - - -
715C GLN 3.3 0.4 - - - -
716C GLN* 1.3 79.4 - - - +
718C PHE* 1.3 78.1 + - + +
719C TYR 3.8 0.7 + - - -
720C GLN 5.3 0.3 + - - -
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Residues in contact with PHE 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C K 2.7 27.7 - - - -
686C ALA* 3.4 48.9 - - + -
689C CYS* 3.6 22.2 - - + -
690C ARG* 3.7 35.0 - - + -
693C GLN* 4.3 1.8 - - - -
703C ILE* 4.0 11.9 - - + -
714C THR* 3.4 25.0 + - + +
715C GLN 3.9 2.5 - - - +
716C GLN 3.4 0.2 - - - -
717C THR* 1.3 82.6 - - + +
719C TYR* 1.3 60.1 + - - +
720C GLN 3.4 2.5 - - - -
721C ASP* 3.3 19.2 + - + +
724C VAL* 3.6 38.4 - - + -
726C TYR* 5.8 2.7 - - + -
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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