Contacts of the helix formed by residues 738 - 746 (chain B) in PDB entry 1N7J
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 GLU 738 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B LEU* 2.9 49.9 - - + +
718B GLU* 4.2 3.8 - - - +
733B PRO 3.8 5.8 - - - +
734B VAL* 3.5 12.5 - - + -
735B SER* 2.8 44.8 + - - +
737B GLU* 1.3 76.0 - - + +
739B VAL* 1.3 57.8 + - - +
741B GLU* 3.5 7.4 + - - +
742B ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 739 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B PHE* 4.6 9.9 - - + -
713B LEU* 4.8 5.4 - - + -
734B VAL* 4.0 15.0 - - + -
735B SER 3.1 15.2 + - - +
736B GLU* 3.1 10.5 + - - +
738B GLU* 1.3 75.6 - - - +
740B ARG* 1.3 65.4 + - - +
742B ALA* 3.3 7.4 + - - +
743B LEU* 3.1 38.5 + - + +
753B LEU* 4.4 8.3 - - + -
773B PHE* 3.7 52.3 - - + -
775B ALA* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 740 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASP* 4.6 6.3 + - - -
253A LEU 5.1 1.0 + - - -
254A ARG* 2.9 63.6 - - - +
736B GLU* 2.9 33.7 + - - +
737B GLU* 3.2 12.2 + - - +
739B VAL* 1.3 77.4 - - - +
741B GLU* 1.3 61.3 + - - +
743B LEU* 3.3 8.7 + - - +
744B VAL* 3.1 29.5 + - + +
750B VAL* 4.1 22.7 - - + +
753B LEU* 3.7 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 741 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B GLN* 4.2 0.4 - - - -
737B GLU 3.0 16.1 + - - +
738B GLU* 3.6 8.3 - - - +
740B ARG* 1.3 74.2 - - - +
742B ALA* 1.3 59.2 + - - +
744B VAL* 3.3 12.9 + - - +
745B ARG* 2.8 84.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 742 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B LEU* 5.6 1.6 - - + -
694B PHE* 3.9 24.0 - - + -
695B GLN* 2.8 23.9 + - + +
698B LEU* 3.6 16.4 - - + -
738B GLU 2.9 18.5 + - - +
739B VAL 3.5 5.8 - - - +
741B GLU* 1.3 75.8 - - - +
743B LEU* 1.3 61.6 + - - +
746B SER* 2.9 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 743 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B LEU* 4.1 8.3 - - + -
711B LEU* 4.1 9.0 - - + -
713B LEU* 4.1 19.5 - - + -
739B VAL* 3.1 28.9 + - + +
740B ARG* 3.5 7.4 - - - +
742B ALA* 1.3 76.8 - - - +
744B VAL* 1.3 61.8 + - - +
746B SER 3.1 8.1 + - - -
747B GLY 3.2 0.5 + - - -
748B TYR* 3.0 47.6 + - + -
750B VAL* 3.7 27.4 - - + -
753B LEU* 5.0 1.1 - - + -
775B ALA* 3.9 26.9 - - + -
777B ALA* 3.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 744 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B ARG* 3.1 20.2 + - + +
741B GLU* 3.7 18.6 - - - +
743B LEU* 1.3 78.4 - - - +
745B ARG* 1.3 60.5 + - + +
747B GLY* 2.9 21.1 + - - -
748B TYR 3.7 16.2 + - - +
749B LYS* 5.9 0.2 - - - -
750B VAL* 4.4 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 745 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B LEU* 5.6 8.5 - - - +
695B GLN* 3.1 43.5 - - - +
699B ASP* 5.0 1.2 - - - +
741B GLU* 2.8 48.9 + - - +
744B VAL* 1.3 79.2 - - + +
746B SER* 1.3 58.3 + - - +
747B GLY* 3.1 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 746 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B GLN* 3.6 4.0 + - - -
698B LEU* 3.3 17.6 - - - +
699B ASP* 2.9 25.9 + - - -
702B THR* 3.9 21.2 - - - +
742B ALA 2.9 18.4 + - - -
743B LEU 3.1 6.7 + - - -
745B ARG* 1.3 74.9 - - - +
747B GLY* 1.3 60.7 + - - +
748B TYR* 3.6 17.9 - - - -
779B LYS* 5.4 1.7 - - - +
----------------------------------------------------------
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