Contacts of the strand formed by residues 173 - 177 (chain B) in PDB entry 2GAO
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 MET 173 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 5.1 0.2 - - - -
119B MET* 3.6 31.6 - - - +
129B ILE* 3.2 27.4 - - + +
131B ILE* 3.8 20.0 - - + -
153B LEU* 3.9 20.0 - - + -
156B GLN* 3.7 40.4 - - + +
157B THR* 3.3 7.9 - - + -
158B THR* 2.8 32.2 + - - +
171B ARG* 3.4 13.5 + - - +
172B PRO* 1.3 75.2 - - - +
174B GLU* 1.3 66.0 + - - +
192B TRP* 3.7 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE 3.2 6.9 + - - +
130B LEU* 3.9 3.3 - - - +
131B ILE* 2.9 29.7 + - - +
148B ARG* 3.2 26.2 + - - -
157B THR* 3.4 11.2 + - - -
158B THR 3.9 1.0 + - - -
159B GLY* 2.7 41.4 + - - +
160B LYS* 3.2 29.8 + - + +
173B MET* 1.3 75.1 - - - +
175B VAL* 1.3 78.8 + - - +
176B PHE* 3.6 12.5 + - + -
192B TRP* 3.5 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 3.4 22.4 - - + +
133B GLY 5.2 0.2 - - - +
144B GLU* 4.1 12.3 - - + -
147B LEU* 4.3 13.0 - - + -
148B ARG* 3.7 22.7 + - + +
153B LEU* 3.2 34.8 - - + -
157B THR* 4.6 1.1 - - + -
160B LYS* 2.7 30.8 + - - -
174B GLU* 1.3 79.7 + - - +
176B PHE* 1.3 61.7 + - - +
177B MET* 3.9 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.5 16.2 - - + -
131B ILE 2.8 9.9 + - - -
132B LEU* 3.3 17.2 - - + +
133B GLY 2.9 22.6 + - - -
160B LYS* 3.8 31.9 - - + +
174B GLU* 3.6 23.8 - - + -
175B VAL* 1.3 79.0 - - - +
177B MET* 1.3 64.1 + - - +
185B GLY 4.2 8.3 - - - +
188B GLU* 3.2 41.3 - - + -
189B GLY* 3.6 21.1 - - - -
192B TRP* 3.4 36.6 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
102B CYS* 3.8 19.7 - - - -
133B GLY* 3.4 10.5 - - - +
136B ILE* 3.8 34.0 - - + +
142B ILE 4.1 6.7 - - - +
143B SER* 4.2 0.9 - - - -
144B GLU* 3.5 60.6 - - + +
147B LEU* 3.9 9.2 - - + -
160B LYS* 4.8 1.8 - - - +
175B VAL* 3.9 13.7 - - - -
176B PHE* 1.3 71.6 - - - +
178B CYS* 1.3 63.5 + - - +
185B GLY* 3.6 16.5 - - - +
----------------------------------------------------------
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