Contacts of the strand formed by residues 191 - 197 (chain A) in PDB entry 6N8Q
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 191 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 2.8 34.4 + - - +
134A VAL* 3.9 3.3 - - + +
147A GLY* 3.8 17.0 - - - -
148A THR 3.0 27.8 + - - +
151A GLY* 3.7 28.0 - - - +
152A ASN 4.3 1.6 - - - +
153A VAL* 4.4 7.0 - - + -
190A MET* 1.3 69.4 - - - +
192A GLU* 1.3 59.5 + - - +
193A ALA 3.5 26.0 - - - +
194A LEU* 4.2 8.7 - - + -
206A ILE* 4.4 6.3 - - + -
207A GLY 3.4 6.5 - - - +
208A TYR* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 6.0 0.7 - - - -
134A VAL* 3.5 13.8 - - - +
190A MET* 3.0 43.8 + - - +
191A VAL* 1.3 74.5 - - - +
193A ALA* 1.3 60.4 + - - +
207A GLY 2.8 9.1 + - - +
209A SER* 3.8 16.7 + - - -
233A LEU* 3.6 31.2 - - + +
234A GLU* 3.8 30.4 - - - +
235A ASN* 4.2 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.3 2.9 - - - -
191A VAL* 3.5 6.7 - - - +
192A GLU* 1.3 79.1 - - - +
194A LEU* 1.3 63.5 + - - +
195A GLN* 4.3 6.5 - - - +
205A LEU* 4.2 8.7 - - + -
206A ILE* 3.5 2.8 - - - -
207A GLY* 2.8 30.5 + - - +
233A LEU* 4.8 2.0 - - + -
235A ASN* 4.7 2.9 - - - +
236A ILE* 3.8 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.7 27.0 - - + +
136A LEU* 3.5 28.1 - - + +
145A TYR* 3.6 27.1 - - + +
147A GLY* 3.5 28.0 - - - +
153A VAL* 3.8 25.1 - - + -
191A VAL* 4.2 3.8 - - + -
193A ALA* 1.3 75.2 - - - +
195A GLN* 1.3 65.3 - - - +
204A ILE* 4.4 9.9 - - + -
205A LEU 3.2 14.6 - - - +
206A ILE* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.6 12.3 - - + +
193A ALA* 4.3 6.2 - - + +
194A LEU* 1.3 82.6 - - - +
196A GLU* 1.3 64.0 + - - +
204A ILE* 3.2 7.6 - - - +
205A LEU* 2.6 40.2 + - + -
235A ASN* 4.5 4.2 + - - -
236A ILE* 2.7 48.1 + - - +
237A TRP* 4.2 5.2 - - - -
238A TRP* 3.7 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.8 15.9 - - + +
137A PRO 4.5 1.6 - - - +
138A HIS* 3.7 22.5 - - + +
139A SER* 2.8 49.2 + - - -
195A GLN* 1.3 76.4 - - - +
197A HIS* 1.3 75.9 + - - +
198A PRO* 3.3 6.8 - - - +
200A ASP 4.4 2.7 - - - +
201A PRO* 3.4 18.5 - - + +
203A GLN 3.8 9.9 - - - +
204A ILE* 4.3 4.5 - - + +
238A TRP* 3.3 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU* 1.3 82.8 - - - +
198A PRO* 1.3 66.9 - - - +
199A ARG* 2.9 46.0 + - + -
200A ASP* 3.1 33.0 + - + +
203A GLN* 2.9 50.0 + - + +
215A ILE* 5.5 0.2 - - + -
238A TRP* 3.3 29.6 - + + -
241A ASP 4.3 3.1 - - - -
242A GLY* 4.0 25.7 + - - -
259A VAL* 5.4 3.7 - - + +
----------------------------------------------------------
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