Contacts of the strand formed by residues 170 - 175 (chain A) in PDB entry 6WNX
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 VAL 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 3.4 17.5 - - - +
132A CYS* 3.7 3.7 - - - -
143A GLY* 3.5 32.5 - - - -
144A LEU 3.1 7.4 + - - +
147A ASN 3.6 23.3 - - - +
148A SER 3.8 11.4 - - - +
149A ILE* 4.1 9.4 - - + -
166A HIS* 3.9 21.8 - - + -
169A SER* 1.3 69.1 - - - +
171A LEU* 1.3 61.0 + - - +
172A CYS 3.8 17.0 - - - +
173A LEU* 4.8 0.4 - - + -
182A THR* 4.0 21.1 - - + -
183A GLY 3.8 4.0 - - - +
184A SER* 4.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 3.6 42.7 - - + +
132A CYS* 3.5 13.8 - - - +
169A SER* 3.8 10.5 - - - +
170A VAL* 1.3 72.2 - - - +
172A CYS* 1.3 63.3 + - - +
183A GLY 2.9 9.2 + - - +
184A SER 3.9 0.4 - - - -
185A SER* 3.5 34.5 - - - +
209A ALA* 4.2 2.5 - - + -
210A VAL 3.5 18.6 - - - +
211A LEU* 3.8 21.4 - - + +
212A HIS* 5.7 0.3 + - - -
334A ARG* 5.7 1.4 + - - -
33C SEP 3.5 27.4 - - - +
34C GLY* 3.9 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A CYS* 3.7 8.5 - - - -
170A VAL* 3.8 2.8 - - - +
171A LEU* 1.3 77.7 - - - +
173A LEU* 1.3 63.5 + - - +
182A THR* 3.4 4.0 - - - -
183A GLY* 3.2 37.0 + - - +
210A VAL 3.8 3.6 - - - -
211A LEU 3.7 12.8 - - - +
212A HIS* 3.6 40.8 - - + +
213A LEU* 3.6 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A CYS* 3.5 17.5 - - + +
133A LEU 4.3 4.1 - - - +
134A GLN* 4.0 32.4 - - + +
141A ILE* 4.1 13.2 - - + +
142A SER* 3.6 17.0 - - - +
143A GLY* 3.5 29.8 - - - +
149A ILE* 4.9 1.6 - - + -
170A VAL* 4.8 0.2 - - + -
172A CYS* 1.3 75.1 - - - +
174A GLN* 1.3 67.6 + - - +
175A TYR* 4.3 9.9 - - + -
180A ILE* 4.6 4.3 - - + -
181A VAL 3.1 14.6 - - - +
182A THR* 3.6 15.3 - - + -
213A LEU* 4.6 6.8 - - - +
384A ARG* 5.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 3.1 18.4 - - - +
173A LEU* 1.3 78.4 - - - +
175A TYR* 1.3 63.5 + - - +
176A ASP* 5.8 0.6 - - - +
180A ILE* 3.6 0.9 - - - +
181A VAL 2.8 31.1 + - - +
213A LEU* 4.3 8.5 - - + +
214A ARG* 3.2 26.6 - - - +
215A PHE* 2.8 73.2 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
134A GLN* 2.8 75.3 + - + -
135A TYR* 3.1 25.2 + - - -
136A ASP* 2.8 30.6 + - + -
139A LYS* 3.6 23.6 + - - +
141A ILE* 3.5 24.2 - - + -
173A LEU* 4.3 4.7 - - + -
174A GLN* 1.3 79.0 + - - +
176A ASP* 1.3 74.2 + - - +
179A VAL 3.0 13.5 - - - +
180A ILE* 3.9 16.8 - - + -
194A VAL* 4.3 1.6 - - + -
215A PHE* 4.1 5.5 - - - -
----------------------------------------------------------
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