Contacts of the strand formed by residues 173 - 179 (chain A) in PDB entry 2IWR
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 ALA 173 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP 3.7 7.0 + - - +
138A ALA* 3.1 18.9 - - + +
139A VAL 3.0 23.7 + - - -
171A GLY 4.1 1.8 + - - -
172A LEU* 1.3 71.9 - - - +
174A LEU* 1.3 60.9 + - - +
205A ARG* 4.0 11.3 - - - +
226A VAL* 4.7 1.8 - - + +
229A LYS* 3.8 34.1 - - + +
230A VAL* 4.2 12.6 - - + +
233A LEU* 4.7 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 3.2 18.2 - - + +
141A PHE* 3.8 16.8 - - + -
158A HIS* 3.9 14.8 - - + +
161A LEU* 4.9 0.2 - - + -
172A LEU* 3.6 37.2 - - + +
173A ALA* 1.3 81.3 - - - +
175A ALA* 1.3 62.4 + - - +
203A MET* 3.5 30.7 - - + +
204A LYS 3.4 15.5 - - - +
205A ARG 2.9 13.5 + - - +
206A CYS* 3.9 11.4 - - + -
207A SER* 3.3 3.1 + - - -
226A VAL* 4.7 4.7 - - - +
229A LYS* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL 3.1 7.5 + - - +
140A ILE* 4.3 15.3 - - + -
141A PHE* 2.8 35.0 + - - +
174A LEU* 1.3 75.4 - - - +
176A LEU* 1.3 57.3 + - - +
177A VAL* 4.2 1.1 - - + -
206A CYS* 3.6 4.3 - - - -
207A SER 3.3 10.5 - - - +
209A TYR* 3.9 16.4 - - + -
222A VAL* 4.5 2.7 - - + -
226A VAL* 3.6 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.4 11.0 - - + +
143A PHE* 3.8 26.0 - - + -
154A VAL* 3.8 28.9 - - + -
175A ALA* 1.3 74.3 - - - +
177A VAL* 1.3 61.6 + - - +
196A ALA* 3.4 27.1 - - - +
199A LEU* 4.1 14.1 - - + -
200A CAF 3.8 13.0 - - - +
203A MET* 4.1 3.1 - - + -
206A CYS* 3.5 13.4 - - - -
207A SER 2.8 7.8 + - - +
208A TYR* 3.3 23.0 - - + -
209A TYR* 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.1 11.9 - - + -
140A ILE* 3.9 15.7 - - + -
141A PHE 2.8 12.7 + - - +
142A VAL* 3.3 8.1 - - + +
143A PHE* 2.9 31.7 + - - +
175A ALA* 4.6 0.7 - - + -
176A LEU* 1.3 79.3 - - - +
178A GLY* 1.3 63.2 + - - +
179A THR* 4.2 4.5 - - + -
209A TYR* 3.3 10.8 - - + +
211A THR* 3.4 37.9 - - + +
222A VAL* 3.9 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE* 3.4 28.5 - - - -
145A LEU* 3.7 12.1 - - - +
177A VAL* 1.3 72.5 - - - +
179A THR* 1.3 64.0 + - - -
208A TYR* 4.0 4.6 - - - -
209A TYR 2.9 10.6 + - - -
210A GLU* 3.1 9.7 - - - +
211A THR 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER 2.7 30.9 + - - +
82A GLY* 4.4 10.9 - - - +
86A LEU* 5.3 4.0 - - + -
142A VAL* 3.5 20.6 - - + -
143A PHE 2.9 10.9 + - - -
144A SER* 3.5 10.4 + - - -
145A LEU* 3.0 26.8 + - - +
177A VAL* 4.2 2.5 - - + -
178A GLY* 1.3 73.7 - - - -
180A GLN* 1.3 61.8 + - - +
181A ASP* 3.8 15.7 + - - +
182A ARG* 5.1 1.2 + - - +
183A ILE* 4.7 1.0 - - - +
211A THR* 3.5 19.1 - - - +
----------------------------------------------------------
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