Contacts of the strand formed by residues 193 - 200 (chain A) in PDB entry 2GF2
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 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLY 3.2 10.1 + - - +
171A LEU 3.2 16.6 - - - -
173A PHE* 3.6 12.8 - - - -
189A LEU 2.9 6.2 + - - -
190A GLY* 3.1 24.8 - - - +
191A CYS 3.7 0.2 - - - -
192A MET* 1.3 80.0 - - - +
194A SER* 1.3 62.7 + - - -
195A ASN 3.5 2.7 - - - -
196A VAL* 4.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLY 3.2 4.8 + - - -
170A ASN* 3.3 44.2 + - - +
171A LEU 2.9 3.3 + - - -
172A THR* 5.3 0.5 + - - -
193A GLY* 1.3 73.5 - - - -
195A ASN* 1.3 76.6 + - - +
196A VAL* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU 3.3 5.5 + - - +
172A THR* 3.3 15.9 + - - +
173A PHE* 2.8 25.7 + - - +
194A SER* 1.3 93.2 + - - +
196A VAL* 1.3 66.7 + - - +
197A VAL* 4.1 1.7 - - + +
246D MET* 3.6 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 3.5 9.6 - - + -
175A VAL* 3.8 13.7 - - + -
182A PHE* 3.6 32.9 - - + -
186A GLN* 4.0 29.5 + - + +
189A LEU* 4.0 21.5 - - + +
190A GLY* 3.9 30.1 - - - +
193A GLY 4.7 3.4 - - - +
194A SER 4.5 0.6 + - - -
195A ASN* 1.3 78.9 + - - +
197A VAL* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR* 4.6 3.1 - - + -
173A PHE 2.8 15.9 + - - +
174A MET* 4.9 1.8 - - + -
175A VAL* 2.8 28.8 + - - +
182A PHE* 3.9 3.1 - - - -
195A ASN* 4.7 1.6 - - + +
196A VAL* 1.3 80.4 - - - +
198A TYR* 1.3 71.5 + - - +
199A CYS* 3.5 4.8 + - - -
239D LEU* 4.0 16.8 - - + -
242D LYS* 5.1 9.6 - - + -
243D ILE* 4.2 18.6 - - + -
246D MET* 3.5 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A MET* 4.3 4.5 - - + -
175A VAL 3.5 11.9 - - - -
177A GLY 2.5 29.4 + - - -
179A GLU* 3.2 47.8 + - + +
182A PHE* 3.7 43.0 - + + -
197A VAL* 1.3 73.1 - - - +
199A CYS* 1.3 58.7 + - - +
200A GLY* 3.1 35.1 + - - -
201A ALA* 4.0 0.5 + - - -
239D LEU* 3.3 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A MET* 3.8 22.7 - - - -
175A VAL 2.7 12.2 + - - +
197A VAL* 3.6 16.4 - - - -
198A TYR* 1.3 74.8 - - - +
200A GLY* 1.3 58.0 + - - +
204A THR* 3.1 36.7 + - - +
208A ALA* 4.0 5.2 - - - -
234D GLY 5.5 0.5 - - - +
235D LEU* 3.7 6.5 - - + +
236D ASP* 5.3 0.7 + - - +
239D LEU* 3.3 24.1 - - + +
243D ILE* 3.7 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL 3.8 0.2 + - - -
176A GLY* 3.2 1.6 - - - -
177A GLY 2.8 31.4 + - - +
198A TYR* 3.1 28.2 + - - -
199A CYS* 1.3 80.0 - - - +
201A ALA* 1.3 57.6 + - - +
204A THR* 3.1 2.4 + - - -
----------------------------------------------------------
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