Contacts of the helix formed by residues 783 - 787 (chain A) in PDB entry 2VWU
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 PRO 783 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739A ARG 3.9 16.2 - - - +
740A ASP* 3.5 21.5 - - + +
744A ARG* 3.5 25.4 - - - +
782A ILE* 1.4 79.1 - - + +
784A ILE* 1.3 62.2 + - - +
785A ARG 3.3 2.7 - - - -
786A TRP* 3.0 27.2 + - + -
787A THR* 2.5 31.6 + - - +
797A PHE* 6.1 0.9 - - + -
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Residues in contact with ILE 784 (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* 3.0 26.6 + - + +
783A PRO* 1.3 70.1 - - - +
785A ARG* 1.3 65.5 + - - +
787A THR* 3.1 24.0 + - - +
792A ILE* 3.8 24.1 - - + +
826A ASN* 3.5 59.9 - - + +
829A VAL* 4.5 9.4 - - + +
830A ILE* 3.9 26.2 - - + -
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Residues in contact with ARG 785 (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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783A PRO 3.3 0.8 - - - -
784A ILE* 1.3 79.6 - - - +
786A TRP* 1.3 93.8 + - + +
787A THR 5.3 0.2 - - - -
804A TRP* 5.0 1.7 + - - -
808A ILE* 3.7 14.7 - - - +
819A ARG* 3.1 34.8 - - - +
820A PRO* 3.0 29.9 + - + +
821A TYR* 3.5 44.4 + - + +
822A TRP 3.2 20.8 + - - -
824A MET 3.0 24.4 + - - -
825A SER* 4.0 0.6 - - - +
826A ASN* 3.2 29.6 + - - +
829A VAL* 4.3 11.4 - - + -
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Residues in contact with TRP 786 (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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740A ASP 6.0 0.2 - - - -
741A LEU 3.5 25.4 - - - +
742A ALA* 3.5 8.5 - - + +
744A ARG* 3.1 33.4 - - - -
783A PRO* 3.0 29.4 + - + +
785A ARG* 1.3 114.4 - - + +
787A THR* 1.3 57.5 + - - +
804A TRP* 3.6 6.2 - - - -
805A SER* 2.7 38.2 + - - +
808A ILE* 3.4 24.3 - - + +
812A GLU* 3.0 37.6 + - - -
819A ARG* 5.4 5.8 - - + -
820A PRO* 3.7 19.3 - - + -
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Residues in contact with THR 787 (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 4.7 3.2 + - - +
782A ILE* 3.4 25.3 - - + +
783A PRO* 2.5 36.0 + - - +
784A ILE 3.1 8.5 + - - +
785A ARG 3.5 0.6 - - - -
786A TRP* 1.3 79.3 - - - +
788A ALA* 1.3 71.0 + - - +
789A PRO* 3.6 1.2 - - - +
791A ALA* 3.6 24.5 - - + -
792A ILE* 3.4 19.9 - - + +
797A PHE* 4.0 10.8 - - + -
801A SER* 6.0 0.4 - - - -
804A TRP* 3.8 9.1 + - - -
805A SER* 4.6 1.8 - - - -
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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