Contacts of the helix formed by residues 717 - 725 (chain P) in PDB entry 1MVW
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 TYR 717 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P GLN* 2.3 30.9 + - - +
715P VAL 3.5 1.2 + - - -
716P LEU* 1.3 66.0 - - - +
718P ALA* 1.3 54.5 + - - +
720P PHE* 2.9 7.4 + - + +
721P LYS* 2.8 24.8 + - - +
740P SER 3.5 15.4 - - - +
741P LYS* 3.9 42.1 - - + +
744P SER* 2.9 36.9 + - - -
745P GLU* 5.7 0.2 - - + -
760P PHE* 3.1 37.9 - + - +
761P GLY 3.3 24.8 + - - -
762P HIS 4.8 0.9 - - - -
763P THR* 3.6 20.4 - - - -
764P MLY 3.6 6.3 - - - -
765P VAL* 3.4 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 718 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P GLN* 2.3 64.7 - - + +
150P GLU* 2.5 29.8 - - + +
717P TYR* 1.3 63.2 - - - +
719P ASP* 1.4 50.6 - - - -
720P PHE 2.8 5.8 + - - -
721P LYS* 2.8 27.7 + - + +
722P GLN* 3.0 18.9 + - - +
740P SER* 4.3 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 719 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P ARG* 4.1 8.6 + - - +
89P GLU* 2.6 32.4 - - - +
93P MET* 5.8 2.5 - - + -
118P TYR* 5.6 1.3 - - - -
148P ARG 2.6 11.5 - - - +
149P GLN* 2.1 51.1 + - + +
151P ALA 3.8 2.9 - - - +
153P PRO* 5.1 0.3 - - - +
715P VAL* 4.1 5.7 - - + +
716P LEU* 3.2 21.1 - - + +
718P ALA* 1.4 70.9 - - - +
720P PHE* 1.4 56.1 + - - +
722P GLN* 4.8 3.0 - - - +
723P ARG* 3.7 22.3 + - - +
724P TYR* 4.9 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 720 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715P VAL* 3.3 32.5 - - + +
716P LEU 2.8 5.0 + - - +
717P TYR* 3.0 17.7 - + + +
718P ALA 2.8 0.2 - - - -
719P ASP* 1.4 79.7 - - - +
721P LYS* 1.3 66.1 + - - +
723P ARG 4.4 0.2 - - - -
724P TYR* 3.4 47.8 + + + +
736P GLN* 3.4 4.8 + - - -
744P SER* 3.3 26.5 - - - +
747P LEU* 4.8 10.8 - - + -
748P LEU* 3.6 36.8 - - + -
765P VAL* 5.5 3.4 - - + -
767P PHE* 3.5 26.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 721 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717P TYR 2.8 8.8 + - - +
718P ALA* 2.8 13.3 + - + +
720P PHE* 1.3 72.6 - - - +
722P GLN* 1.3 63.2 + - - +
724P TYR 2.9 2.6 + - - -
725P ARG* 2.7 21.4 + - - +
733P PRO 3.9 0.9 - - - -
736P GLN* 0.8 219.1 + - + +
737P PHE* 2.1 27.1 + - + +
740P SER* 4.0 13.2 - - - +
743P ALA* 3.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 722 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P GLU* 3.1 39.1 + - - +
18P ARG* 3.9 18.5 - - - +
21P GLU* 5.6 3.1 - - - +
24P ARG* 4.5 18.4 + - - +
149P GLN 5.7 1.3 + - - +
718P ALA 3.0 10.2 + - - +
719P ASP* 5.2 3.4 - - - +
721P LYS* 1.3 80.7 - - - +
723P ARG* 1.3 70.8 + - + +
724P TYR 3.3 0.3 + - - -
725P ARG* 3.9 9.8 + - - +
726P VAL* 4.9 6.4 - - - +
736P GLN* 3.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 723 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P ARG* 4.4 25.3 - - - +
25P ILE* 5.9 3.4 - - - +
28P GLN* 2.3 50.0 + - - +
84P MLY 4.2 26.2 - - - +
719P ASP 3.7 15.9 + - - +
720P PHE 4.1 0.4 + - - -
721P LYS 3.3 1.0 - - - -
722P GLN* 1.3 86.3 - - + +
724P TYR* 1.3 78.5 + - + +
726P VAL* 5.2 6.1 - - - +
727P LEU* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 724 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P MLY 1.3 83.4 + - - -
715P VAL* 5.7 4.5 - - + -
719P ASP 5.0 2.7 - - - -
720P PHE* 3.5 51.4 - + + +
721P LYS 2.9 2.8 + - - -
723P ARG* 1.3 98.8 - - + +
725P ARG* 1.3 67.6 + - - +
726P VAL* 3.0 4.9 - - - -
727P LEU* 2.8 47.8 + - + +
736P GLN* 4.9 0.4 - - - +
747P LEU* 3.7 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 725 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721P LYS 2.7 19.1 + - - +
722P GLN* 3.9 8.0 + - - +
723P ARG 3.9 0.4 - - - -
724P TYR* 1.3 70.3 - - - +
726P VAL* 1.3 55.9 + - + +
727P LEU 2.8 12.0 + - - -
729P ALA* 2.9 21.8 + - - +
732P ILE* 3.3 19.4 - - - +
733P PRO* 2.0 60.9 - - + +
734P GLU* 6.1 0.4 - - - +
736P GLN* 3.4 7.8 - - - +
737P PHE* 2.7 33.5 - - - -
----------------------------------------------------------
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