Contacts of the helix formed by residues 985 - 990 (chain A) in PDB entry 3NZ0
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 SER 985 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A IZA 4.8 5.4 - - - -
983A LEU 3.9 0.7 + - - +
984A GLY* 1.3 75.2 - - - -
986A LEU* 1.3 59.4 + - - +
987A ARG* 3.5 6.9 + - - +
988A ASP* 3.2 34.5 + - - +
989A TYR* 3.0 29.7 + - - +
1026A ALA 4.0 2.5 - - - -
1027A ARG* 3.4 26.3 + - - +
1029A VAL 3.1 10.3 - - - -
1030A LEU* 3.9 9.3 - - - +
1031A LEU* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 986 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984A GLY 4.1 0.2 + - - -
985A SER* 1.3 69.3 - - - +
987A ARG* 1.3 66.0 + - - +
989A TYR* 4.2 3.8 - - + -
990A LEU* 3.0 40.9 + - + +
1003A PHE* 3.6 42.0 - - + -
1007A ILE* 4.1 13.0 - - + -
1026A ALA* 3.6 16.6 + - + +
1029A VAL* 2.8 37.2 + - + +
1031A LEU* 4.0 23.0 - - + +
1037A VAL* 4.5 2.9 - - + -
1094A LEU* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 987 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985A SER* 3.2 3.7 - - - +
986A LEU* 1.3 79.5 - - - +
988A ASP* 1.3 71.0 + - - +
991A PRO* 3.0 24.5 - - - +
1026A ALA* 3.3 5.4 + - + -
1027A ARG* 3.5 62.6 - - + +
1093A GLU* 4.9 4.9 - - - +
1098A CYS* 3.7 38.8 + - + +
1100A SER* 3.8 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 988 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A IZA 5.8 4.0 - - - -
983A LEU 5.5 3.6 - - - +
984A GLY* 5.8 0.8 - - - -
985A SER* 3.2 24.8 + - - +
987A ARG* 1.3 94.9 + - - +
989A TYR* 1.3 63.5 + - - +
991A PRO* 3.8 8.3 - - - +
992A ARG* 3.8 24.9 + - - +
1027A ARG* 5.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 989 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983A LEU* 4.2 38.7 + - + +
985A SER 3.0 17.7 + - - +
986A LEU* 3.2 3.8 + - + +
988A ASP* 1.3 78.9 - - - +
990A LEU* 1.3 77.6 + - + +
992A ARG* 3.3 9.8 + - - +
993A HIS* 2.8 61.9 + + - -
995A ILE* 4.0 21.1 - - + -
1003A PHE* 4.6 6.1 - + - -
1031A LEU* 3.6 29.6 - - + -
1035A ARG* 3.0 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 990 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A LEU* 3.0 35.7 + - + +
989A TYR* 1.3 79.7 - - + +
991A PRO* 1.3 69.0 - - + +
992A ARG 3.2 0.2 + - - -
993A HIS 2.9 22.5 - - - +
995A ILE* 4.3 16.2 - - + -
1000A LEU* 3.7 25.1 - - + -
1003A PHE* 4.3 4.3 - - + -
1094A LEU* 3.4 40.8 - - + -
1097A HIS* 3.7 28.5 + - - +
1098A CYS* 3.9 15.7 - - + -
----------------------------------------------------------
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