Contacts of the helix formed by residues 782 - 792 (chain Y) in PDB entry 3ZPV
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 THR 782 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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776Y ARG* 3.7 1.6 - - - +
780Y GLY 4.7 1.6 - - - +
781Y LEU* 1.3 75.7 - - - +
783Y GLU* 1.3 64.6 + - - +
784Y ALA* 3.7 8.0 + - - +
785Y ALA* 3.0 18.2 + - - +
786Y PHE* 3.0 22.3 + - - +
332Z ASN* 2.9 38.7 + - + +
335Z ALA* 4.8 1.7 - - - +
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Residues in contact with GLU 783 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801A LYS* 4.4 25.2 - - - +
762Y GLU* 4.8 9.8 - - - +
776Y ARG* 3.5 31.6 + - - +
782Y THR* 1.3 73.7 - - - +
784Y ALA* 1.3 63.1 + - - +
786Y PHE* 3.5 6.0 + - + +
787Y GLN* 3.1 46.8 + - + +
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Residues in contact with ALA 784 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A HIS* 5.6 1.3 - - - +
782Y THR* 3.2 6.8 + - - +
783Y GLU* 1.3 77.0 - - - +
785Y ALA* 1.3 60.7 + - - +
787Y GLN* 3.3 12.2 + - - +
788Y MET* 3.0 39.3 + - + +
335Z ALA* 4.0 8.7 - - + -
339Z LEU* 3.9 28.9 - - + -
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Residues in contact with ALA 785 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781Y LEU* 4.2 3.8 - - + -
782Y THR* 3.0 12.7 + - - +
784Y ALA* 1.3 75.6 - - - +
786Y PHE* 1.3 58.4 + - - +
788Y MET* 3.3 2.6 + - - +
789Y LEU* 2.9 36.4 + - - +
331Z ALA* 3.5 29.3 - - + +
332Z ASN* 3.1 29.4 - - - +
335Z ALA* 3.7 10.6 - - + +
346Z ILE* 5.4 0.2 - - - +
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Residues in contact with PHE 786 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762Y GLU* 3.8 28.7 - - + -
763Y ALA 3.4 43.1 - - - -
764Y VAL* 4.0 17.3 - - + -
776Y ARG* 3.4 28.3 - - + -
781Y LEU* 4.5 7.7 - - + +
782Y THR 3.0 16.1 + - - +
783Y GLU* 3.6 7.9 - - + +
785Y ALA* 1.3 78.3 - - - +
787Y GLN* 1.3 69.1 + - + +
789Y LEU* 3.8 4.1 - - + +
790Y ASN* 3.1 53.9 + - - +
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Residues in contact with GLN 787 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783Y GLU* 3.1 42.8 + - - +
784Y ALA* 3.3 12.6 + - - +
786Y PHE* 1.3 84.5 - - + +
788Y MET* 1.3 60.4 + - + +
790Y ASN* 3.6 5.7 + - - +
791Y LYS* 3.1 38.7 + - - +
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Residues in contact with MET 788 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784Y ALA* 3.0 20.9 + - + +
785Y ALA* 3.9 4.0 - - - +
787Y GLN* 1.3 76.6 - - + +
789Y LEU* 1.3 66.8 + - - +
791Y LYS* 3.3 17.7 + - + +
792Y GLU* 3.1 44.3 + - - +
335Z ALA* 3.6 37.7 - - + +
338Z VAL* 3.8 32.3 - - + -
339Z LEU* 3.9 22.9 - - + -
346Z ILE* 4.0 17.0 - - + -
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Residues in contact with LEU 789 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764Y VAL* 5.1 4.7 - - + -
781Y LEU* 4.1 15.3 - - + -
785Y ALA 2.9 21.3 + - - +
786Y PHE* 3.8 4.7 - - - +
788Y MET* 1.3 76.4 - - - +
790Y ASN* 1.3 68.3 + - - +
791Y LYS 3.2 0.7 + - - -
792Y GLU 3.4 16.6 - - - +
795Y ALA* 4.1 13.9 - - + +
796Y GLU 4.5 9.9 - - - +
797Y TRP* 4.1 25.8 - - + +
326Z PHE* 4.0 28.3 - - + -
331Z ALA* 3.8 20.0 - - + -
346Z ILE* 3.9 20.4 - - + +
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Residues in contact with ASN 790 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763Y ALA 5.1 2.3 + - - +
764Y VAL* 5.0 5.7 - - - +
786Y PHE* 3.1 56.6 + - - +
787Y GLN* 3.9 6.8 - - - +
789Y LEU* 1.3 83.0 - - - +
791Y LYS* 1.3 59.8 + - + +
792Y GLU 3.7 1.9 + - - -
793Y VAL* 5.7 0.5 - - - -
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Residues in contact with LYS 791 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787Y GLN* 3.1 25.5 + - - +
788Y MET* 3.9 18.4 - - + +
789Y LEU 3.2 0.4 - - - -
790Y ASN* 1.3 77.8 - - - +
792Y GLU* 1.3 83.4 + - - +
793Y VAL* 3.5 3.8 + - - +
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Residues in contact with GLU 792 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788Y MET* 3.1 38.7 + - - +
789Y LEU 3.4 11.0 + - - +
790Y ASN 4.8 1.3 - - - -
791Y LYS* 1.3 98.7 - - - +
793Y VAL* 1.3 65.5 + - - +
794Y PHE 3.1 1.6 - - - +
795Y ALA* 3.0 27.1 + - + +
345Z THR* 4.4 22.9 - - + +
346Z ILE* 3.6 26.4 + - + +
347Z ILE* 4.2 14.8 - - + -
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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