Contacts of the helix formed by residues 782 - 792 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3176 GLY* 4.0 32.3 - - - +
7569 GLU* 5.1 6.1 - - - +
776I ARG* 3.6 1.6 - - - +
780I GLY 4.7 1.1 - - - +
781I LEU* 1.3 75.4 - - - +
783I GLU* 1.3 66.5 + - - +
784I ALA* 3.7 7.3 + - - +
785I ALA* 3.0 19.8 + - - +
786I PHE* 3.0 21.3 + - - +
332J ASN* 2.9 36.9 + - + +
335J ALA* 4.7 3.1 - - - +
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Residues in contact with GLU 783 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762I GLU* 4.9 9.8 - - - +
776I ARG* 3.5 32.2 + - - +
782I THR* 1.3 73.5 - - - +
784I ALA* 1.3 61.4 + - - +
786I PHE* 3.5 7.2 + - + +
787I GLN* 3.1 44.9 + - - +
751U GLY 4.9 3.3 - - - +
754U HIS* 3.8 25.8 - - + +
772U PHE* 6.1 0.9 - - - -
801U LYS* 3.5 24.1 + - - -
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Residues in contact with ALA 784 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782I THR* 3.2 7.4 + - - +
783I GLU* 1.3 78.5 - - - +
785I ALA* 1.3 65.7 + - - +
787I GLN* 3.3 12.2 + - - +
788I MET* 3.0 35.5 + - + +
335J ALA* 4.1 9.0 - - + -
339J LEU* 4.0 23.8 - - + -
754U HIS* 3.8 20.7 + - + -
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Residues in contact with ALA 785 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781I LEU* 4.2 4.3 - - + -
782I THR* 3.0 13.4 + - - +
784I ALA* 1.3 76.4 - - - +
786I PHE* 1.3 57.7 + - - +
788I MET* 3.3 3.2 + - - +
789I LEU* 2.9 37.1 + - - +
331J ALA* 3.5 28.3 - - + +
332J ASN* 3.2 28.3 - - - +
335J ALA* 3.7 9.5 - - + +
346J ILE* 5.2 0.2 - - - +
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Residues in contact with PHE 786 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762I GLU* 3.8 28.5 - - + -
763I ALA 3.5 43.5 - - - -
764I VAL* 4.0 17.3 - - + -
776I ARG* 3.4 28.7 - - + -
781I LEU* 4.5 7.5 - - + +
782I THR 3.0 17.1 + - - +
783I GLU* 3.6 8.1 - - + +
785I ALA* 1.3 78.0 - - - +
787I GLN* 1.3 68.4 + - + +
789I LEU* 3.8 4.9 - - + +
790I ASN* 3.0 54.3 + - - +
791K LYS* 4.2 17.0 - - + -
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Residues in contact with GLN 787 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783I GLU* 3.1 34.4 + - + +
784I ALA* 3.3 6.3 + - - +
786I PHE* 1.3 87.4 - - + +
788I MET* 1.3 59.3 + - + +
790I ASN* 3.5 5.6 + - - +
791I LYS* 3.1 40.1 + - - +
752U MET 4.9 4.4 + - - +
754U HIS* 3.9 26.2 + - - -
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Residues in contact with MET 788 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784I ALA* 3.0 21.8 + - + +
785I ALA* 3.9 3.8 - - - +
787I GLN* 1.3 77.9 - - + +
789I LEU* 1.3 66.9 + - - +
791I LYS* 4.4 20.9 - - + +
792I GLU* 3.1 31.8 + - + +
335J ALA* 3.7 34.1 - - + +
338J VAL* 3.7 35.4 - - + -
339J LEU* 4.2 18.8 - - + -
345J THR* 6.1 0.2 - - - -
346J ILE* 3.8 25.4 - - + +
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Residues in contact with LEU 789 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764I VAL* 5.1 3.1 - - + -
781I LEU* 4.1 23.6 - - + -
785I ALA 2.9 21.2 + - - +
786I PHE* 3.8 4.5 - - + +
788I MET* 1.3 77.1 - - - +
790I ASN* 1.3 69.3 + - - +
791I LYS 3.2 0.3 + - - -
792I GLU 3.4 16.8 - - - +
795I ALA* 4.1 13.8 - - + +
796I GLU* 4.5 9.9 - - - +
797I TRP* 4.1 17.7 - - + -
326J PHE* 3.9 29.4 - - + -
331J ALA* 3.9 19.5 - - + -
346J ILE* 3.9 19.7 - - + -
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Residues in contact with ASN 790 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763I ALA 5.1 1.8 + - - +
764I VAL* 5.0 5.4 - - - +
786I PHE* 3.0 58.1 + - - +
787I GLN* 3.8 6.6 - - - +
788I MET 3.2 0.2 - - - -
789I LEU* 1.3 80.5 - - - +
791I LYS* 1.3 59.9 + - + +
792I GLU 3.7 2.3 + - - +
793I VAL* 5.7 0.5 - - - -
790K ASN* 3.2 53.0 + - + +
791K LYS* 3.8 12.1 + - + +
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Residues in contact with LYS 791 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787I GLN* 3.1 26.7 + - - +
788I MET* 3.9 23.5 - - + +
789I LEU 3.2 0.4 - - - -
790I ASN* 1.3 78.4 - - - +
792I GLU* 1.3 76.9 + - - +
793I VAL* 3.6 4.3 + - - +
761K ASP 5.4 3.8 - - - +
762K GLU* 5.6 2.1 - - + -
763K ALA 5.1 1.6 + - - +
786K PHE* 4.2 17.5 - - + -
790K ASN* 4.0 16.0 + - - +
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Residues in contact with GLU 792 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788I MET* 3.1 21.3 + - + +
789I LEU 3.4 10.5 - - - +
790I ASN 3.4 1.5 - - - -
791I LYS* 1.3 92.9 - - + +
793I VAL* 1.3 67.6 + - - +
794I PHE* 3.1 3.6 + - - -
795I ALA* 3.0 27.2 + - + +
345J THR* 3.5 26.6 - - - +
346J ILE* 4.1 16.4 - - + +
347J ILE* 4.3 13.4 - - + +
759K ASP* 3.0 23.2 - - - +
760K ASN* 5.5 0.5 - - - -
761K ASP 5.0 3.6 - - - +
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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