Contacts of the helix formed by residues 123 - 131 (chain A) in PDB entry 1OFY
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 ASP 123 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 3.4 36.6 - - + +
122A ARG* 1.3 77.4 + - - +
124A GLU* 1.3 67.3 + - - +
125A ALA* 3.6 13.1 + - - +
126A TRP* 3.0 26.7 + - - +
127A CYS* 3.1 13.0 + - - -
220A LYS* 5.8 1.7 - - - -
1296A HEC 5.5 1.4 - - - +
1302A ACT 3.9 12.6 - - - -
123B ASP* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP* 1.3 75.0 - - - +
125A ALA* 1.3 57.3 + - - +
127A CYS* 3.1 6.4 + - - +
128A ALA* 2.9 30.8 + - - +
1302A ACT 3.5 26.3 - - + +
121B LYS* 5.5 8.1 + - - -
220B LYS* 5.7 2.1 - - - +
232B SER 4.4 1.2 - - - +
233B PRO* 3.4 24.3 - - + +
234B LEU* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP* 3.2 13.3 + - - +
124A GLU* 1.3 79.3 - - - +
126A TRP* 1.3 59.1 - - - +
128A ALA* 3.5 6.7 + - - +
129A THR* 3.0 24.8 + - - -
219A ASN* 3.3 20.5 + - - +
220A LYS* 3.8 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A HIS* 5.5 2.9 - + + -
98A VAL* 3.9 36.3 - - + -
122A ARG* 3.6 44.6 - - + +
123A ASP* 3.0 25.1 + - - +
125A ALA* 1.3 74.6 - - - +
127A CYS* 1.3 67.9 + - - +
129A THR* 3.1 22.7 + - - -
217A PHE* 3.7 26.0 - + - -
219A ASN* 4.9 1.3 - - - +
1296A HEC 3.5 43.0 + - + +
1297A HEC 3.4 68.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 4.2 4.9 - - + -
123A ASP 3.1 18.5 + - - -
124A GLU 3.1 4.2 + - - +
126A TRP* 1.3 76.0 - - - +
128A ALA* 1.3 58.9 + - - +
130A CYS* 3.1 5.4 + - - +
131A HIS* 2.9 29.6 + - - -
1297A HEC 1.8 74.9 - - + -
1302A ACT 4.1 13.5 - - - -
233B PRO* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 6.3 0.4 - - + -
124A GLU 2.9 16.8 + - - +
125A ALA* 4.0 8.5 - - - +
126A TRP 3.2 0.2 - - - -
127A CYS* 1.3 73.1 - - - +
129A THR* 1.3 66.4 + - - +
130A CYS 3.1 0.6 + - - -
131A HIS* 3.4 24.7 - - - +
132A ASN* 3.4 10.7 - - - +
233B PRO* 6.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA 3.0 17.3 + - - -
126A TRP 3.1 10.3 + - - -
128A ALA* 1.3 78.7 - - - +
130A CYS* 1.3 59.0 + - - +
132A ASN* 3.6 14.9 + - - +
216A ALA* 3.5 30.7 - - + +
217A PHE* 3.6 39.1 - - + -
219A ASN* 3.0 15.6 + - - +
1295A HEC 4.0 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.6 20.8 - - + +
127A CYS 3.1 3.0 + - - -
129A THR* 1.3 79.8 - - - +
131A HIS* 1.3 55.4 + - - +
132A ASN* 2.7 33.2 + - - +
217A PHE* 4.1 9.2 - - - -
1295A HEC 3.8 16.4 - - - -
1297A HEC 1.8 88.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 3.4 25.9 - - + +
31A LYS* 2.8 44.6 + - + +
32A PRO 3.9 7.2 - - - -
33A VAL* 3.5 8.8 - - + +
127A CYS 2.9 27.6 + - - +
128A ALA* 3.4 18.3 - - - +
130A CYS* 1.3 66.5 - - - +
132A ASN* 1.3 56.0 + - - +
133A ILE 4.0 0.9 - - - -
1297A HEC 1.9 94.0 + + + -
233B PRO* 6.1 0.2 - - + -
----------------------------------------------------------
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