Contacts of the helix formed by residues 787 - 792 (chain D) in PDB entry 6V3O
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 HIS 787 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781D TRP* 3.2 12.9 + - - -
782D THR* 3.2 34.9 + - + +
785D ARG* 3.6 18.1 + - - -
786D PHE* 1.3 75.7 + - - +
788D LEU* 1.3 66.2 + - - +
789D PRO* 3.3 7.9 - - - -
790D VAL* 2.9 18.5 + - + +
791D TRP* 3.1 11.8 - - + +
832D VAL* 3.7 24.6 + - + +
835D LYS 2.7 37.3 + - - -
836D GLY* 3.6 7.8 - - - -
864D TYR* 5.5 2.4 - - + -
966D MET* 3.1 26.0 - - + +
969D THR* 4.1 11.2 - - + +
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Residues in contact with LEU 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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728D TYR* 5.1 0.4 - - + -
731D VAL* 5.0 0.2 - - + -
732D VAL* 4.8 0.4 - - + -
738D PHE* 4.5 10.1 - - + -
777D TRP* 4.0 25.6 - - + -
781D TRP* 4.2 20.0 - - + +
786D PHE* 3.2 25.4 + - + -
787D HIS* 1.3 75.0 - - - +
789D PRO* 1.3 74.4 - - + +
790D VAL 3.0 1.6 + - - -
791D TRP* 3.3 15.0 + - + +
792D LEU* 3.0 65.5 + - + +
860D LEU* 4.1 26.2 - - + -
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Residues in contact with PRO 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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605D GLY 4.9 5.7 - - - +
609D GLY* 5.1 0.2 - - - -
610D ARG* 4.3 16.5 + - - +
728D TYR* 4.8 11.4 - - + -
777D TRP* 3.3 46.2 - - + +
778D ILE* 3.8 18.7 - - + +
781D TRP* 3.5 30.3 - - + -
787D HIS* 3.3 6.1 - - - -
788D LEU* 1.3 99.4 - - + +
790D VAL* 1.3 60.0 + - + +
792D LEU* 4.6 1.5 + - - -
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Residues in contact with VAL 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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610D ARG* 3.1 35.8 - - - +
778D ILE* 5.0 4.3 - - + -
782D THR* 6.1 0.2 - - - +
787D HIS* 2.9 16.0 + - + +
789D PRO* 1.3 84.9 - - + +
791D TRP* 1.3 60.5 + - + +
794D VAL* 4.8 0.7 - - - +
828D LEU* 3.8 22.7 - - + -
829D LEU* 3.2 29.9 - - + +
832D VAL* 4.1 25.4 - - + -
969D THR* 4.5 3.1 - - - +
970D GLY* 3.9 28.0 - - - +
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Residues in contact with TRP 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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786D PHE* 2.9 36.3 + + - -
787D HIS* 3.1 28.6 + - + -
788D LEU* 3.6 15.3 - - + -
790D VAL* 1.3 80.6 - - + +
792D LEU* 1.3 93.8 + - + +
793D GLY 3.2 0.8 + - - -
794D VAL* 3.1 23.9 + - - +
829D LEU* 4.1 11.0 - - + -
832D VAL* 5.4 2.9 - - + -
833D PHE* 3.7 37.2 - + + -
860D LEU* 3.6 21.5 - - - -
863D LYS* 3.9 10.8 - - + -
864D TYR* 3.7 37.6 - + + -
867D THR* 3.8 19.5 - - + +
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Residues in contact with LEU 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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609D GLY* 4.2 10.6 - - - -
610D ARG 4.4 4.0 + - - -
724D ALA* 5.7 0.2 - - - +
727D GLU* 5.1 2.2 - - + +
728D TYR* 3.5 50.0 - - + +
731D VAL* 4.1 12.8 - - + -
732D VAL* 3.6 21.1 - - + -
788D LEU* 3.0 45.2 + - + +
789D PRO 4.6 1.3 - - - +
790D VAL 3.8 0.8 - - - -
791D TRP* 1.3 99.5 - - + +
793D GLY* 1.3 59.9 + - - +
794D VAL* 3.8 2.1 + - - +
860D LEU* 4.6 12.6 - - + -
863D LYS* 4.6 10.5 - - + -
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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