Contacts of the helix formed by residues 784 - 794 (chain D) in PDB entry 3VI7
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 ILE 784 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624D TYR* 3.8 28.5 - - + -
740D TRP* 4.3 9.6 - - + -
746D VAL* 4.0 36.6 - - + -
751D PHE* 4.1 11.9 - - + -
780D LYS 3.6 10.7 + - - +
781D VAL* 3.3 23.3 + - - +
783D ALA* 1.3 76.1 - - - +
785D PRO* 1.4 75.8 - - + +
786D ALA* 4.1 6.7 - - + +
787D VAL* 3.0 9.4 + - + -
788D ALA 2.9 19.6 + - - -
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Residues in contact with PRO 785 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783D ALA 3.5 10.1 - - - +
784D ILE* 1.4 85.7 - - + -
786D ALA* 1.4 56.9 + - - +
788D ALA* 3.3 7.2 + - + +
789D ASN* 3.0 29.6 + - - +
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Residues in contact with ALA 786 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623D ALA* 3.5 30.3 - - - +
624D TYR* 3.9 16.8 - - + +
784D ILE* 3.3 6.5 - - + +
785D PRO* 1.4 78.3 - - - +
787D VAL* 1.3 62.5 + - - +
789D ASN* 3.6 7.7 + - - +
790D TRP* 3.2 21.5 + - - +
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Residues in contact with VAL 787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D TYR* 3.8 36.3 - - + +
623D ALA* 5.1 1.3 - - - -
624D TYR* 4.5 8.3 - - + +
751D PHE* 4.1 26.5 - - + -
781D VAL* 3.5 25.4 - - + +
782D GLN* 4.4 0.2 - - - -
784D ILE* 3.0 23.6 + - + +
786D ALA* 1.3 74.1 - - - +
788D ALA* 1.3 61.4 + - - +
790D TRP* 3.2 6.6 + - + +
791D ILE* 2.9 43.2 + - + +
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Residues in contact with ALA 788 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782D GLN 3.2 23.0 + - - +
783D ALA* 4.6 4.7 - - - +
784D ILE 2.9 9.9 + - - +
785D PRO* 3.5 13.2 - - + +
787D VAL* 1.3 76.4 - - - +
789D ASN* 1.3 56.0 + - - +
791D ILE* 3.4 5.8 + - - +
792D LYS* 3.0 33.7 + - - +
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Residues in contact with ASN 789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785D PRO 3.0 16.6 + - - +
786D ALA* 3.8 7.1 + - - +
787D VAL 3.2 0.2 - - - -
788D ALA* 1.3 77.0 - - - +
790D TRP* 1.3 62.7 + - - +
792D LYS* 3.6 14.9 + - - +
793D ARG* 3.0 66.5 + - - +
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Residues in contact with TRP 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D GLU* 2.8 24.8 + - - -
619D ARG* 3.5 31.3 - - + +
620D TYR* 3.7 28.4 - + - -
623D ALA* 3.8 18.4 - - + -
629D TYR* 3.8 19.7 - + - -
631D ASP* 3.9 6.5 - - + -
633D ARG* 3.8 17.3 - - - -
786D ALA 3.2 12.6 + - - +
787D VAL* 3.2 9.6 + - + +
789D ASN* 1.3 78.0 - - - +
791D ILE* 1.3 64.9 + - - +
793D ARG* 3.1 26.8 + - - +
794D ARG* 2.9 59.6 + - + +
795D PRO* 4.6 2.2 - - + -
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Residues in contact with ILE 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620D TYR* 3.8 25.6 - - + +
754D GLU* 4.1 4.0 - - - +
782D GLN* 3.8 35.9 - - + +
787D VAL* 2.9 33.9 + - + +
788D ALA* 3.8 5.2 - - - +
790D TRP* 1.3 75.7 - - + +
792D LYS* 1.3 64.8 + - - +
793D ARG 3.4 0.2 + - - -
794D ARG* 3.5 40.9 + - - +
796D GLN* 4.1 6.2 - - - +
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Residues in contact with LYS 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C THR* 6.4 0.2 - - - +
522C TYR* 4.5 13.5 + - - -
788D ALA 3.0 19.7 + - - +
789D ASN* 3.7 17.5 - - - +
791D ILE* 1.3 79.9 - - - +
793D ARG* 1.3 63.2 + - + +
794D ARG 3.8 2.8 + - - +
796D GLN* 4.9 2.6 - - - +
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Residues in contact with ARG 793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789D ASN* 3.0 52.4 + - - +
790D TRP* 3.1 30.4 + - + +
792D LYS* 1.3 82.2 - - + +
794D ARG* 1.3 66.3 + - - +
795D PRO* 3.8 2.4 - - - +
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Residues in contact with ARG 794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D ARG* 3.8 25.6 - - - +
616D GLU* 2.8 40.7 + - - +
620D TYR* 3.0 26.1 + - - -
633D ARG* 5.0 0.9 - - - +
754D GLU* 5.1 3.4 + - - -
758D THR* 4.9 12.3 + - - +
790D TRP* 2.9 39.3 + - + +
791D ILE* 3.5 41.5 + - - +
792D LYS 3.6 2.5 - - - +
793D ARG* 1.3 81.8 - - - +
795D PRO* 1.3 74.9 + - + +
796D GLN* 3.0 29.0 + - - +
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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