Contacts of the helix formed by residues 744 - 753 (chain B) in PDB entry 1M2V
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 744 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 3.5 37.9 - - - +
591B ASP 3.6 26.5 - - - +
592B GLN* 4.3 1.3 - - - +
593B SER* 3.6 10.5 - - - -
743B LEU* 1.4 89.5 - - + +
745B LEU* 1.3 67.2 + - - +
746B LYS* 3.3 3.4 - - + +
747B TYR* 2.9 31.7 + - + -
748B LEU 2.9 17.7 + - - -
865B VAL* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 745 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ARG* 3.6 44.4 - - - +
206B VAL* 4.4 19.5 - - + -
208B ARG* 5.1 2.8 - - - +
593B SER* 4.2 6.5 + - - -
649B LEU* 3.9 21.8 - - + +
650B ALA* 4.4 7.0 - - - +
653B SER* 3.9 26.7 - - - +
743B LEU 3.6 2.2 + - - -
744B PRO* 1.3 71.5 - - - +
746B LYS* 1.3 63.6 + - - +
748B LEU* 3.1 18.6 + - + -
749B ILE* 3.3 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 746 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B PRO* 4.7 2.9 - - + +
745B LEU* 1.3 79.6 - - - +
747B TYR* 1.3 88.7 + - + +
749B ILE* 4.1 4.1 + - - +
750B LYS* 3.9 14.2 + - - +
862B HIS* 4.9 7.1 + - - -
863B ASP* 5.4 2.0 + - - -
864B ASP* 3.4 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 747 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B LEU* 4.0 18.4 - - + -
744B PRO* 2.9 23.0 + - + +
746B LYS* 1.3 99.2 + - + +
748B LEU* 1.3 67.7 + - - +
749B ILE 3.0 2.2 - - - -
750B LYS* 3.2 25.9 + - - +
751B ASN* 3.1 26.6 + - - +
805B GLY* 5.9 2.9 - - - -
862B HIS* 3.6 31.5 + + - -
864B ASP* 2.5 44.8 + - - -
865B VAL* 3.4 34.3 - - + +
867B THR* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 748 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B SER* 3.6 36.8 - - - +
656B ASN* 3.2 38.6 - - + +
740B LEU* 3.5 30.7 - - + +
743B LEU* 4.1 17.4 - - + +
744B PRO 2.9 12.7 + - - +
745B LEU* 3.1 18.1 + - + +
747B TYR* 1.3 77.1 - - - +
749B ILE* 1.3 64.9 + - + +
751B ASN* 3.3 3.6 - - - +
752B ILE* 3.2 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 749 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.9 38.1 - - + +
649B LEU* 4.0 33.7 - - + +
652B ALA* 4.6 4.7 - - + -
713B LEU* 4.0 21.1 - - + -
745B LEU* 3.3 33.6 + - + +
746B LYS* 4.3 4.9 - - - +
747B TYR 3.0 0.6 - - - -
748B LEU* 1.3 79.8 - - + +
750B LYS* 1.3 62.8 + - - +
751B ASN 3.0 4.5 - - - -
752B ILE* 3.0 9.3 + - + +
753B TYR 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 750 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746B LYS 3.9 10.3 + - - +
747B TYR* 3.2 28.6 + - - +
749B ILE* 1.3 78.4 - - - +
751B ASN* 1.3 59.4 + - - +
753B TYR 3.6 8.1 - - - -
754B PRO* 3.3 19.6 - - - +
755B ASP* 3.4 22.7 - - - +
803B ASP* 2.9 44.9 + - - +
804B ASN* 3.6 6.1 - - - -
805B GLY* 3.4 22.3 + - - +
859B LEU* 4.6 1.6 + - - +
862B HIS* 4.0 21.0 + - - -
869B GLN* 3.9 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 751 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B HIS* 3.2 33.4 + - - -
739B ASN* 5.0 2.4 + - - +
740B LEU* 3.9 10.2 - - + +
743B LEU* 3.2 30.1 - - + +
747B TYR* 3.1 10.5 + - - +
748B LEU 3.3 11.7 - - - +
749B ILE 3.0 0.2 - - - -
750B LYS* 1.3 79.9 - - - +
752B ILE* 1.3 62.6 + - - +
754B PRO* 4.8 1.9 - - - +
804B ASN* 3.3 22.6 + - - +
805B GLY* 4.3 7.5 + - - -
806B ASN* 3.3 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 752 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B ALA* 5.3 5.4 - - + +
656B ASN* 4.6 4.7 - - + +
713B LEU* 3.4 37.7 - - + +
714B MET* 5.3 3.8 - - + -
716B SER* 3.4 23.8 - - - +
717B LEU* 3.6 37.5 - - + +
720B HIS* 4.5 6.5 - - + +
740B LEU* 5.1 3.4 - - + -
748B LEU* 3.2 37.5 - - + +
749B ILE* 3.0 15.1 + - + +
751B ASN* 1.3 82.0 - - + +
753B TYR* 1.3 55.4 + - - +
754B PRO* 3.9 2.7 - - - +
903B VAL* 3.9 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 753 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 3.3 28.3 - - + +
154B LEU* 3.9 20.3 - - + +
712B LEU* 3.8 22.2 - - + -
713B LEU* 4.2 18.6 - - + -
716B SER* 3.9 17.0 - - - +
749B ILE* 2.9 14.7 + - - +
750B LYS* 3.4 9.2 - - - +
752B ILE* 1.3 75.8 - - - +
754B PRO* 1.3 80.5 - - - +
755B ASP* 4.6 3.8 - - - +
787B ILE 4.6 2.7 - - - -
788B ASN* 3.2 7.4 - - - -
789B ALA* 2.8 27.6 + - + -
903B VAL* 4.0 6.3 - - + -
904B GLU* 2.4 40.7 + - + -
----------------------------------------------------------
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