Contacts of the helix formed by residues 711 - 718 (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 GLY 711 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A HIS* 3.3 32.1 - - - -
705A ASP* 3.6 1.8 + - - -
709A HIS 3.5 3.4 + - - -
710A HIS* 1.3 71.2 - - - +
712A ASN* 1.3 63.8 + - - -
713A GLY 3.1 3.6 - - - -
714A THR* 3.1 4.4 + - - -
715A GLN* 3.1 20.3 + - - +
726A TYR* 3.2 25.3 + - - -
728A SER* 4.3 0.2 + - - -
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Residues in contact with ASN 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A HIS* 2.9 54.9 + - - +
672A ASP* 4.4 10.4 + - - +
677A MET* 3.6 15.8 - - - +
710A HIS* 2.9 17.9 + - - -
711A GLY* 1.3 71.3 - - - +
713A GLY* 1.3 70.0 + - - +
715A GLN* 3.5 2.5 + - - +
716A GLN* 3.1 23.9 + - - +
739A PRO* 3.7 13.9 - - + +
741A SER* 3.3 22.9 - - - +
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Residues in contact with GLY 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A HIS 2.9 10.6 + - - -
671A ALA 3.3 28.5 - - - -
672A ASP* 3.9 9.6 - - - -
683A ASN* 3.5 5.2 - - - -
712A ASN* 1.3 81.4 - - - +
714A THR* 1.3 61.2 + - - +
716A GLN* 3.2 5.2 + - - +
717A THR* 3.1 26.8 + - - -
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Residues in contact with THR 714 (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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669A HIS* 3.6 15.6 + - - +
683A ASN* 2.9 25.2 + - - +
685A VAL* 5.3 2.7 - - + +
686A ALA* 5.0 1.8 - - + -
703A ILE* 3.8 27.6 - - + -
705A ASP* 4.8 0.3 + - - -
711A GLY 3.1 4.8 + - - -
713A GLY* 1.3 75.1 - - - +
715A GLN* 1.3 64.3 + - - +
717A THR* 3.5 3.1 + - - -
718A PHE* 3.3 37.4 + - + +
726A TYR* 3.4 36.0 - - + -
797A SER* 4.8 3.1 + - - -
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Residues in contact with GLN 715 (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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710A HIS* 2.9 39.6 + - + +
711A GLY 3.1 6.9 + - - +
712A ASN 3.8 8.0 + - - +
713A GLY 3.3 0.2 - - - -
714A THR* 1.3 78.2 - - - +
716A GLN* 1.3 63.5 + - - +
718A PHE 3.5 1.3 + - - -
719A TYR* 3.1 42.6 + - + +
726A TYR* 4.1 5.7 - - + -
741A SER* 5.1 2.8 - - - -
742A GLY 4.7 0.2 - - - +
746A GLU* 2.6 28.0 + - - +
756A ASN* 2.9 38.5 + - - +
758A ASN* 3.0 10.1 + - - +
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Residues in contact with GLN 716 (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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672A ASP* 3.5 24.2 + - + +
673A HIS* 3.0 37.9 + - - +
712A ASN 3.1 14.7 + - - +
713A GLY* 3.5 7.4 - - - +
715A GLN* 1.3 79.2 - - - +
717A THR* 1.3 67.0 + - - +
718A PHE 3.3 0.5 + - - -
719A TYR* 3.4 17.0 + - - +
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Residues in contact with THR 717 (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* 3.8 32.6 + - + +
672A ASP* 5.5 1.0 - - - -
673A HIS* 5.5 2.3 + - - -
683A ASN* 4.9 0.2 + - - -
686A ALA* 4.3 3.0 - - + +
690A ARG* 3.0 51.9 + - - +
713A GLY 3.1 16.5 + - - -
714A THR 3.9 4.7 - - - -
715A GLN 3.4 0.2 - - - -
716A GLN* 1.3 85.9 + - - +
718A PHE* 1.3 77.5 + - + +
719A TYR 3.7 0.5 + - - -
720A GLN 5.2 0.5 + - - -
721A ASP* 5.4 0.5 - - - +
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Residues in contact with PHE 718 (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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202A K 2.5 29.8 - - - -
686A ALA* 3.6 40.8 - - + -
689A CYS* 3.7 22.7 - - + -
690A ARG* 3.7 33.9 - - + -
693A GLN* 4.6 1.1 - - - -
703A ILE* 3.5 22.9 - - + -
714A THR* 3.3 32.3 + - + +
715A GLN 3.8 1.8 - - - -
716A GLN 3.2 0.2 - - - -
717A THR* 1.3 81.7 - - + +
719A TYR* 1.3 59.8 + - - +
720A GLN 3.1 4.6 + - - -
721A ASP* 3.3 13.5 + - - +
724A VAL* 3.6 32.3 - - + -
726A TYR* 5.4 6.1 - - + -
756A ASN* 5.7 1.3 - - - +
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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