Contacts of the strand formed by residues 173 - 183 (chain A) in PDB entry 2OM5
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 GLY 173 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 4.6 3.8 - - - -
141A ASN* 3.7 11.7 - - - -
171A ASP 3.4 3.8 + - - -
172A LEU* 1.3 78.5 - - - +
174A ASN* 1.3 71.6 - - - +
175A TYR* 3.6 10.8 - - - -
196A GLN* 4.8 1.6 + - - +
197A LEU* 3.4 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU 3.6 1.2 - - - +
140A LEU* 3.7 3.5 - - - +
141A ASN* 2.7 44.3 + - - +
173A GLY* 1.3 78.0 - - - +
175A TYR* 1.3 62.9 + - - +
194A PHE* 3.5 27.5 + - + +
195A ALA 3.3 9.6 - - - +
196A GLN* 3.0 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 5.3 0.2 - - - +
123A LEU* 4.2 15.9 - - + -
138A TRP* 3.8 18.5 - + + -
139A LEU 3.5 4.0 - - - -
140A LEU* 3.7 14.2 - - + +
147A ILE* 3.6 32.1 - - + -
153A HIS* 5.5 3.1 - + - -
162A LEU* 4.1 19.5 - - + -
164A ILE* 5.2 4.0 - - + +
171A ASP* 2.4 46.7 + - - +
173A GLY 3.6 18.4 - - - -
174A ASN* 1.3 78.9 - - - +
176A SER* 1.3 60.9 + - - +
192A SER* 4.6 0.2 + - - -
193A LYS 3.8 1.2 - - - +
194A PHE* 3.3 3.4 - - - -
195A ALA* 2.7 45.1 + - + +
197A LEU* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TRP* 3.2 10.1 - - - -
139A LEU* 2.8 40.2 + - - +
175A TYR* 1.3 75.7 - - - +
177A CYS* 1.3 60.1 + - - +
178A LEU 3.8 0.5 + - - -
191A PHE* 3.5 15.4 - - - +
192A SER* 3.2 35.1 + - - -
193A LYS 4.2 0.4 - - - -
194A PHE* 3.4 28.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.3 10.8 - - + -
110A ARG* 5.3 0.4 - - - +
125A CYS* 2.0 52.7 - - + +
136A TYR* 4.2 10.5 - - - -
137A ARG 4.0 1.8 - - - -
138A TRP* 3.6 27.5 - - + -
160A GLY 3.7 11.2 - - - -
176A SER* 1.3 73.3 + - - +
178A LEU* 1.3 62.4 + - - +
179A ALA 3.9 0.2 - - - -
191A PHE* 3.1 3.3 - - - -
192A SER* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER 3.8 0.3 - - - +
136A TYR* 3.5 4.2 - - - -
137A ARG* 2.7 49.8 + - + +
139A LEU* 3.8 15.9 - - + -
143A PHE* 3.7 19.5 - - + -
146A PHE* 3.6 29.4 - - + -
176A SER 3.8 1.0 + - - -
177A CYS* 1.3 73.6 - - - +
179A ALA* 1.3 59.4 + - - +
180A THR* 3.9 17.4 + - - +
189A SER* 4.2 17.0 - - - +
190A VAL 3.4 5.2 - - - +
191A PHE* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 5.0 1.8 - - + -
105A PHE* 4.4 11.4 - - + -
127A PRO* 4.8 2.9 - - + -
134A LEU* 3.8 26.2 - - + -
135A SER 3.5 4.9 - - - -
136A TYR* 4.0 13.5 - - + -
177A CYS 3.9 1.4 - - - -
178A LEU* 1.3 73.0 - - - +
180A THR* 1.3 59.2 + - - +
181A SER 4.3 0.2 - - - -
188A LYS 3.8 0.9 - - - +
189A SER* 3.2 1.9 - - - -
190A VAL* 2.7 55.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.3 7.9 - - - +
135A SER* 2.8 48.6 + - - -
137A ARG* 5.7 1.5 - - - +
178A LEU* 3.9 13.0 + - - +
179A ALA* 1.3 72.4 - - - +
181A SER* 1.3 62.7 + - - +
182A HIS* 3.5 16.0 + - + +
187A THR* 3.5 27.6 - - + -
188A LYS 3.2 4.3 - - - +
189A SER* 2.6 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE 5.2 1.7 + - - -
102A LEU* 4.1 17.2 - - - +
131A TYR 4.9 2.4 + - - -
132A PRO* 4.3 16.3 + - - +
133A GLY 4.6 2.3 + - - -
134A LEU* 3.6 21.9 - - - +
180A THR* 1.3 72.1 - - - +
182A HIS* 1.3 68.3 + - - +
183A MET* 4.7 6.4 + - - +
186A SER 3.7 1.8 - - - +
187A THR* 3.2 6.6 - - - +
188A LYS* 2.7 44.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO* 4.9 9.0 - - - +
133A GLY 4.9 5.6 + - - +
135A SER* 3.5 26.9 + - - -
137A ARG* 6.0 0.7 - - - -
180A THR* 3.5 23.5 + - + +
181A SER* 1.3 75.9 + - - +
183A MET* 1.3 63.3 + - - +
186A SER 4.1 1.3 - - - -
187A THR* 3.6 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.6 43.7 - - + +
19A PRO* 3.8 33.7 - - + -
100A GLY* 3.8 19.7 - - - +
131A TYR 5.5 0.9 - - - +
132A PRO* 5.0 4.3 - - + -
181A SER* 4.0 8.3 + - - +
182A HIS* 1.3 75.9 - - - +
184A ASP* 1.3 72.2 + - + +
185A PHE 3.1 3.5 + - - +
186A SER* 3.0 41.8 + - - +
----------------------------------------------------------
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