Contacts of the strand formed by residues 193 - 204 (chain A) in PDB entry 6QPA
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 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS* 2.8 31.4 + - - +
183A LEU* 3.6 31.9 - - + +
186A MET* 3.6 28.0 - - + +
187A LYS* 3.7 19.8 - - - +
190A VAL 3.5 15.6 + - - +
191A PRO 3.3 2.2 + - - -
192A GLY* 1.3 74.1 - - - +
194A VAL* 1.3 65.4 + - - +
195A GLY 3.9 14.8 - - - +
196A TRP* 3.8 13.9 - - + -
257A ILE* 3.8 19.5 - - + -
259A TRP* 3.5 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PRO* 3.4 17.7 - - + +
151A LYS* 3.4 10.9 - - + +
152A VAL 3.8 17.9 - - - +
153A ALA* 3.5 35.4 - - + +
158A ARG* 4.6 4.3 - - + -
187A LYS* 3.3 15.7 - - - -
192A GLY* 3.7 13.7 - - - +
193A MET* 1.3 74.1 - - - +
195A GLY* 1.3 59.8 + - - +
258A GLU* 2.8 27.0 + - + +
259A TRP 3.8 3.4 - - - +
260A GLU* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP 3.2 13.2 - - - -
126A LEU* 4.0 6.7 - - - -
127A PRO* 4.0 7.0 - - - -
187A LYS* 4.0 7.2 - - - -
193A MET* 3.7 3.4 - - - +
194A VAL* 1.3 82.0 - - - +
196A TRP* 1.3 67.9 + - - +
257A ILE* 3.5 6.8 - - - +
258A GLU* 2.9 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LYS* 3.4 46.4 - - + -
124A SER* 3.4 5.9 - - - -
125A ASP* 2.9 57.0 + - + +
126A LEU* 3.6 9.9 - - - +
180A THR* 4.5 12.6 - - + -
183A LEU* 3.6 49.9 + - + -
184A GLU* 3.9 25.3 - - + +
187A LYS* 3.9 13.3 - - + +
193A MET* 3.8 22.0 - - + -
195A GLY* 1.3 76.8 - - - +
197A MET* 1.3 70.7 + - - +
198A ILE* 3.8 15.9 - - + -
256A HIS 3.0 12.6 - - - +
257A ILE* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.8 24.5 - - + -
79A TYR* 4.0 6.1 - - + -
121A VAL* 3.8 25.4 - - + -
123A LYS 3.5 6.5 - - - -
124A SER* 4.1 5.2 - - - -
126A LEU* 3.9 24.5 - - + -
183A LEU* 5.2 0.2 - - - -
196A TRP* 1.3 79.1 - - - +
198A ILE* 1.3 65.2 + - - +
199A MET* 3.7 32.5 - - + -
254A LEU 3.8 0.3 - - - +
255A VAL* 3.7 3.6 - - - +
256A HIS* 2.8 57.7 + - + +
308A TRP* 4.0 11.2 - - + -
312A LEU* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU 3.6 0.3 - - - +
121A VAL* 3.6 4.2 - - - -
122A VAL* 2.8 48.0 + - + -
123A LYS* 2.9 17.0 + - + +
175A PHE* 4.6 8.7 - - + -
176A GLU* 4.1 6.3 - - + +
179A ALA* 3.9 10.3 - - + -
180A THR* 3.4 39.7 - - - +
183A LEU* 3.7 20.6 - - + -
196A TRP* 3.8 14.6 - - + -
197A MET* 1.3 71.4 - - - +
199A MET* 1.3 62.9 + - - +
253A TYR* 3.9 22.9 - - + -
254A LEU 4.0 3.4 - - - +
255A VAL* 4.9 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.0 13.7 - - - -
10A ILE* 3.8 22.0 - - + -
79A TYR* 3.5 24.5 - - - +
119A PHE* 3.8 20.6 - - + -
120A GLU 3.2 6.3 - - - +
121A VAL* 4.8 4.3 - - + -
162A ILE* 5.2 1.3 - - + -
197A MET* 3.7 32.5 - - + +
198A ILE* 1.3 78.2 - - - +
200A LYS* 1.3 60.1 + - - +
253A TYR* 3.2 7.8 - - - +
254A LEU* 2.7 60.6 + - + +
256A HIS* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.3 3.7 - - - -
120A GLU* 2.9 47.5 + - + +
122A VAL* 3.7 11.9 - - + +
172A GLU* 4.5 9.3 - - - +
176A GLU* 3.8 8.7 + - - +
199A MET* 1.3 72.7 - - - +
201A GLN* 1.3 70.2 + - - +
202A PHE* 3.4 8.4 + - + -
251A THR* 3.9 21.1 - - + -
252A GLN 3.7 3.4 - - - -
253A TYR* 3.5 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TRP* 5.2 3.8 + - - +
117A PRO* 3.8 20.9 - - + +
118A TYR 3.4 12.6 - - - +
119A PHE* 3.5 15.3 - - + -
200A LYS* 1.3 79.8 - - - +
202A PHE* 1.3 62.2 + - - +
203A GLY 3.9 9.2 - - - +
204A VAL* 3.8 13.3 - - - +
247A GLY* 3.6 8.6 - - - -
248A GLN* 3.0 41.9 + - - +
251A THR* 4.3 9.5 - - - +
252A GLN* 2.7 55.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.9 18.6 - - + -
85A VAL* 3.8 21.5 - - + -
118A TYR* 3.1 16.0 + - + -
119A PHE 3.5 28.3 - - - -
120A GLU* 3.6 26.5 - - + +
200A LYS* 3.8 7.2 - - + +
201A GLN* 1.3 74.0 - - - +
203A GLY* 1.3 57.9 + - - +
243A PRO* 3.7 29.7 - - + +
246A PRO* 5.0 0.9 - - - +
247A GLY* 3.6 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO* 3.3 6.1 - - - +
118A TYR* 2.6 32.8 + - - +
201A GLN* 3.8 1.4 - - - +
202A PHE* 1.3 79.7 - - - +
204A VAL* 1.3 62.1 + - - +
243A PRO* 3.6 15.0 - - - +
245A ILE 3.4 12.3 - - - -
247A GLY* 3.5 10.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TRP* 3.7 40.4 - - + -
116A GLU 3.5 10.8 - - - +
117A PRO* 3.9 7.2 - - + -
118A TYR* 3.9 4.5 - - - -
201A GLN* 3.8 16.8 - - - +
203A GLY* 1.3 78.3 - - - +
205A SER* 1.3 67.2 + - - +
209A SER* 3.4 22.4 - - - +
243A PRO* 3.6 1.4 - - - +
244A PRO* 3.2 20.8 - - - +
245A ILE* 2.9 35.7 + - + +
246A PRO 4.2 4.5 - - - +
----------------------------------------------------------
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