Contacts of the helix formed by residues 1096 - 1100 (chain A) in PDB entry 1OFD
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 LEU1096 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 5.9 0.2 - - - -
210A ASN* 5.7 0.2 - - - -
211A THR* 4.0 14.4 - - - +
1046A ALA* 3.6 39.0 - - + +
1049A ALA* 4.2 6.7 - - + +
1050A LYS* 4.1 14.1 - - + -
1091A LEU* 2.8 22.6 + - + +
1094A ASN* 3.7 26.2 - - + +
1095A GLN* 1.3 79.3 - - - +
1097A ARG* 1.3 65.1 + - - +
1098A ASP* 3.3 6.3 - - - -
1099A ARG* 3.0 61.0 + - - +
1100A VAL* 4.1 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1097 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088A HIS* 3.0 23.1 + - - -
1091A LEU* 3.4 26.9 + - - -
1092A MET* 3.7 33.7 - - + +
1095A GLN* 3.6 2.4 - - - +
1096A LEU* 1.3 78.1 - - - +
1098A ASP* 1.3 58.2 + - - +
1099A ARG 3.3 0.2 + - - -
1100A VAL* 2.9 52.5 + - - +
1102A LEU* 3.5 18.5 - - - +
1121A GLY 2.8 26.9 + - - -
1123A GLU* 2.8 29.1 + - - -
1234A TRP* 3.6 36.3 - - + +
1237A HIS* 3.8 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1098 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A GLN 4.0 9.0 - - - +
1096A LEU 3.7 8.5 - - - -
1097A ARG* 1.3 74.1 + - - +
1099A ARG* 1.3 73.7 + - - +
1100A VAL 3.3 0.4 - - - -
1233A GLN 4.7 2.2 - - - +
1234A TRP* 3.4 30.0 - - + +
1236A ASN 3.9 13.2 - - - +
1237A HIS* 2.8 25.8 + - - +
1238A GLU 4.9 1.6 + - - -
1241A HIS* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1099 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A CYS 5.7 1.8 + - - -
35A SER 4.4 2.2 + - - -
36A ALA* 4.1 16.2 + - - +
38A ASN* 2.9 35.4 + - - +
1049A ALA* 4.2 16.5 + - + +
1050A LYS* 4.5 17.4 + - - +
1052A ASN* 6.4 0.4 - - - +
1053A ALA 3.5 1.2 - - - +
1054A ASP 3.8 3.1 - - - +
1095A GLN 4.7 4.9 + - - -
1096A LEU* 3.0 47.5 + - - +
1098A ASP* 1.3 90.7 + - - +
1100A VAL* 1.3 67.8 + - + +
1237A HIS* 4.5 2.1 - - - +
1241A HIS* 2.7 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A ALA* 4.1 16.2 - - + -
1053A ALA* 3.4 29.8 - - + +
1054A ASP 3.2 7.9 - - - +
1056A ILE* 3.7 28.3 - - + -
1091A LEU* 3.5 34.3 - - + -
1096A LEU 4.8 1.3 - - - +
1097A ARG* 2.9 28.9 + - - +
1098A ASP 3.3 0.6 - - - -
1099A ARG* 1.3 79.2 - - - +
1101A LEU* 1.3 63.6 + - - +
1102A LEU* 3.9 8.1 - - + -
1237A HIS* 3.0 11.9 - - - -
----------------------------------------------------------
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