Contacts of the helix formed by residues 788 - 795 (chain A) in PDB entry 2VWV
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 ALA 788 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786A TRP 4.0 0.4 + - - -
787A THR* 1.3 77.8 - - - +
789A PRO* 1.3 74.3 - - + +
790A GLU* 3.3 26.9 - - - +
791A ALA* 3.0 4.3 + - + +
792A ILE* 3.0 19.6 + - - +
801A SER* 3.8 16.7 + - - -
804A TRP* 3.7 28.6 - - + +
864A ARG* 3.7 5.6 - - - +
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Residues in contact with PRO 789 (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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787A THR 3.5 2.9 - - - +
788A ALA* 1.3 86.5 - - + +
790A GLU* 1.3 61.4 + - + +
792A ILE* 3.3 12.4 + - + +
793A ALA* 2.8 28.5 + - - +
804A TRP* 3.6 31.2 - - + -
833A ILE* 3.7 28.3 - - + -
838A ARG* 5.4 1.3 - - - +
859A LYS* 5.5 12.3 - - + +
864A ARG* 4.8 2.0 - - - +
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Residues in contact with GLU 790 (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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788A ALA* 3.3 15.5 - - - +
789A PRO* 1.3 75.7 - - - +
791A ALA* 1.3 59.0 + - + +
793A ALA* 4.3 4.5 - - - +
794A PHE* 2.9 58.3 + - + +
796A LYS 4.4 2.9 - - - +
798A THR* 4.9 0.2 + - - -
801A SER* 4.0 7.3 - - - -
859A LYS 4.6 3.5 - - - +
861A ARG* 3.3 29.2 - - - +
864A ARG* 2.8 43.6 + - - -
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Residues in contact with ALA 791 (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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782A ILE* 4.3 3.9 - - - +
787A THR* 3.5 18.4 - - + -
788A ALA 3.0 9.9 + - - +
790A GLU* 1.3 78.8 - - - +
792A ILE* 1.3 61.2 + - - +
795A ARG* 2.8 30.5 + - - -
796A LYS 3.2 23.1 + - - +
797A PHE* 3.8 15.7 - - + -
801A SER* 4.1 16.8 - - - -
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Residues in contact with ILE 792 (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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782A ILE* 4.3 14.5 - - + +
784A ILE* 3.8 48.0 - - + +
787A THR* 3.6 32.3 - - + +
788A ALA 3.0 12.8 + - - +
789A PRO* 3.5 10.5 - - + +
791A ALA* 1.3 78.0 - - - +
793A ALA* 1.3 64.5 + - - +
795A ARG* 3.8 4.9 + - - +
830A ILE* 4.3 24.2 - - + -
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Residues in contact with ALA 793 (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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789A PRO 2.8 19.6 + - - +
790A GLU* 3.5 5.1 + - - +
791A ALA 3.4 0.2 - - - -
792A ILE* 1.3 78.0 - - - +
794A PHE* 1.3 80.5 + - + +
795A ARG 3.8 0.2 + - - -
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Residues in contact with PHE 794 (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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790A GLU* 2.9 42.1 + - + +
793A ALA* 1.3 88.4 - - + +
795A ARG* 1.3 70.1 + - - +
796A LYS* 3.1 25.6 + - + +
861A ARG* 6.1 2.9 - - - -
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Residues in contact with ARG 795 (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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739A ARG* 5.6 0.7 + - - -
782A ILE* 4.0 22.7 - - + -
791A ALA 2.8 17.6 + - - -
792A ILE 3.8 3.2 + - - +
793A ALA 3.5 2.6 + - - -
794A PHE* 1.3 78.6 - - - +
796A LYS* 1.3 61.3 + - - +
797A PHE* 4.1 15.9 - - + -
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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