Contacts of the helix formed by residues 643 - 647 (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 GLY 643 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D TYR* 3.5 29.4 - - - -
640D GLY 3.5 4.9 + - - -
641D ARG 3.3 5.3 + - - -
642D GLY* 1.3 80.5 - - - +
644D THR* 1.3 62.3 + - - -
645D VAL* 3.1 8.1 - - - -
646D GLY* 2.9 23.2 + - - +
647D ARG* 4.1 4.5 + - - +
673D GLN* 4.5 1.7 + - - +
828D LEU* 4.7 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 644 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D TYR* 4.5 10.7 + - + -
610D ARG* 5.8 3.1 - - - +
642D GLY 3.7 1.0 + - - -
643D GLY* 1.3 72.5 - - - -
645D VAL* 1.3 64.0 + - - +
646D GLY 3.0 1.6 + - - -
647D ARG* 3.5 24.6 + - - +
651D PRO 4.7 0.2 - - - -
652D THR* 3.9 3.5 + - - +
655D ALA* 3.5 14.1 + - - +
658D SER* 5.6 0.2 + - - -
659D GLN* 4.9 5.9 + - - -
824D VAL* 3.4 42.9 - - + +
825D THR* 4.6 8.7 - - + +
828D LEU* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 645 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D TYR* 4.3 2.5 - - - +
639D HIS* 3.6 41.1 - - + +
640D GLY 5.6 0.4 - - - +
643D GLY* 4.3 10.3 - - - -
644D THR* 1.3 76.3 + - - +
646D GLY* 1.3 58.8 + - - +
647D ARG 3.4 0.9 - - - -
652D THR* 3.1 20.5 - - - +
655D ALA* 4.0 11.9 - - + +
656D ILE* 3.8 27.4 - - + -
659D GLN* 4.0 26.0 - - + +
668D ILE* 5.4 1.1 - - + -
670D VAL* 3.6 21.7 - - + +
694D PHE* 4.0 6.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 646 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643D GLY* 2.9 17.6 + - - -
645D VAL* 1.3 79.1 - - - +
647D ARG* 1.3 55.8 + - - +
648D GLY* 3.1 12.0 + - - -
670D VAL* 4.3 10.5 - - - -
671D THR 4.4 9.8 - - - +
672D VAL* 5.9 0.5 - - - -
673D GLN* 4.9 13.2 + - - +
676D VAL* 4.1 19.4 - - - +
694D PHE* 5.7 0.7 - - - -
968D ASN* 5.2 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 647 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643D GLY 4.3 7.0 - - - +
644D THR* 3.5 23.1 - - - +
646D GLY* 1.3 76.1 - - - +
648D GLY* 1.3 48.5 + - - +
649D GLY 2.4 21.4 + - - -
650D GLY 4.7 0.4 - - - -
651D PRO* 3.6 40.5 - - + +
652D THR* 3.3 5.0 - - + +
676D VAL* 5.2 5.7 - - - +
679D PHE* 5.5 0.5 - - - -
680D CYS* 4.8 0.7 - - - -
824D VAL* 4.6 4.9 + - - +
827D ASP* 3.9 13.1 + - - +
828D LEU* 3.7 36.1 - - + +
831D MET* 3.6 35.0 - - + +
887D LEU* 4.4 8.3 - - - +
968D ASN* 3.8 20.6 - - - +
1001D PG0 3.1 36.2 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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