Contacts of the helix formed by residues 174 - 181 (chain B) in PDB entry 2W77
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 ARG 174 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR* 3.5 3.1 + - - +
142B GLU* 3.9 30.5 - - + +
143B ASP 5.3 0.2 - - - +
173B THR* 1.3 73.6 - - - +
175B GLN* 1.3 57.2 + - - +
177B MET* 3.2 36.7 + - - +
178B ASP* 2.7 46.6 + - - +
182B LEU 4.8 3.8 + - - -
183B ASN* 6.0 1.4 - - - +
240B MET* 3.4 13.3 + - - +
241B ALA* 4.8 1.2 - - - +
243B TYR 2.9 28.6 + - - -
244B ASP* 3.2 22.7 + - - +
271B LYS* 3.5 17.7 - - - +
1818B PO4 3.2 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR 4.5 3.6 + - - +
143B ASP* 5.4 4.7 + - - +
145B GLY* 3.4 41.0 + - - +
146B SER 3.8 18.4 - - - +
147B TYR* 3.9 12.1 - - + -
173B THR* 3.2 1.0 + - - -
174B ARG* 1.3 77.0 - - - +
176B ASN* 1.3 66.2 - - - +
178B ASP* 3.5 12.8 + - - +
179B ASP* 2.7 58.8 + - - +
768B ARG* 4.0 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TYR* 3.8 22.8 - - + -
172B VAL* 3.9 13.9 - - + +
173B THR* 3.1 21.4 + - - +
175B GLN* 1.3 79.9 - - - +
177B MET* 1.3 63.4 + - - +
178B ASP 3.2 0.3 + - - -
179B ASP 3.2 1.6 + - - -
180B PHE* 3.0 41.0 + - - +
182B LEU* 3.7 12.7 - - - +
191B HIS* 4.6 8.8 - - - +
688B GLN* 3.2 30.5 + - - +
716B TYR* 5.2 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 4.1 24.2 - - + +
173B THR 3.1 10.1 + - - +
174B ARG* 3.2 45.3 - - - +
176B ASN* 1.3 76.9 - - - +
178B ASP* 1.3 58.5 + - - +
181B GLY* 2.8 26.9 + - - -
182B LEU* 3.0 26.3 + - + +
183B ASN* 5.5 0.2 + - - -
188B VAL* 4.1 20.6 - - + -
240B MET* 3.5 36.3 - - + +
243B TYR* 3.8 12.3 - - + +
244B ASP 4.9 0.2 - - - +
245B ARG* 4.5 10.3 - - - -
246B VAL* 4.6 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG* 2.7 47.7 + - - +
175B GLN* 3.8 15.6 + - - +
177B MET* 1.3 73.4 - - - +
179B ASP* 1.3 67.9 + - - +
180B PHE 3.0 0.9 + - - -
181B GLY* 3.1 11.7 + - - -
282B GLU* 6.0 0.7 - - - -
768B ARG* 4.8 5.1 + - - +
780B ASN* 5.4 0.3 - - - +
812B ARG* 3.6 15.4 + - - +
1818B PO4 2.7 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TYR* 2.5 36.4 + - - +
175B GLN* 2.7 43.2 + - - +
178B ASP* 1.3 77.6 - - - +
180B PHE* 1.3 69.2 + - + +
181B GLY 3.7 0.2 + - - -
718B SER* 3.5 10.4 + - - -
729B THR* 5.4 1.6 - - - +
766B MET* 3.3 24.7 - - + +
768B ARG* 2.8 33.7 + - - +
778B SER* 5.9 0.3 - - - -
780B ASN* 3.0 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TYR* 3.6 23.1 - + - -
176B ASN* 3.0 32.9 + - - +
179B ASP* 1.3 82.6 - - + +
181B GLY* 1.3 64.2 + - - +
182B LEU* 3.1 23.2 + - + +
191B HIS* 3.8 18.2 + + - +
716B TYR* 4.1 25.1 - + + -
717B THR 3.9 9.9 - - - -
718B SER* 5.1 0.4 - - - -
731B GLY* 5.1 0.9 - - - -
732B GLY* 3.7 32.8 - - - -
764B ASP* 4.5 11.9 - - + -
765B LEU 6.0 0.2 - - - -
766B MET* 4.4 12.1 - - + -
780B ASN* 3.4 25.4 + - - +
782B ASN* 5.2 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B MET 2.8 9.0 + - - -
178B ASP 3.1 9.4 + - - -
179B ASP 3.5 0.2 - - - -
180B PHE* 1.3 77.7 - - - +
182B LEU* 1.3 61.6 + - - +
183B ASN* 3.0 29.9 + - - +
187B ASP* 3.5 6.2 - - - +
780B ASN* 4.2 6.0 - - - +
808B MET* 5.9 7.3 - - - +
----------------------------------------------------------
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