Contacts of the strand formed by residues 180 - 190 (chain A) in PDB entry 6JBQ
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 180 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.3 41.7 - - + +
48A LEU* 5.1 2.7 - - + -
51A MET* 6.1 0.2 - - + -
178A SER* 2.8 26.4 + - - +
179A PRO* 1.3 83.8 - - + +
181A GLU* 1.3 61.7 + - - +
183A ILE* 3.8 24.5 - - + -
205A MET* 3.8 32.1 - - + -
206A GLU 3.7 6.1 - - - +
207A THR* 4.2 7.6 - - + +
216A ALA* 4.8 4.5 - - + -
535D ARG* 2.9 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLY* 5.9 2.6 - - - -
176A CYS* 4.0 10.7 - - - -
179A PRO 5.2 0.2 - - - -
180A VAL* 1.3 78.3 - - - +
182A ARG* 1.3 59.3 + - - +
183A ILE* 4.3 0.7 - - - -
206A GLU* 2.8 15.6 + - + +
207A THR 4.1 9.0 - - - +
208A ASN* 3.9 29.5 - - + +
528D THR* 6.0 1.2 - - - +
531D LYS* 3.5 38.2 - - + +
532D GLU* 3.1 27.1 + - - +
535D ARG* 3.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A HIS* 3.3 32.1 - - - -
181A GLU* 1.3 81.8 - - - +
183A ILE* 1.3 63.5 + - - +
184A ALA* 4.0 19.2 - - - +
204A GLU* 3.8 28.2 + - - +
205A MET* 3.4 4.6 - - - +
206A GLU* 2.7 51.0 + - + +
531D LYS* 3.8 30.8 - - + +
534D GLU* 3.5 21.8 - - - +
581D MET* 3.7 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 4.0 41.2 - - + +
47A LEU* 3.7 41.1 - - + -
48A LEU* 5.4 8.4 - - + +
180A VAL* 3.8 25.4 - - + -
182A ARG* 1.3 80.1 - - - +
184A ALA* 1.3 66.4 + - - +
185A TYR* 5.8 2.5 - - + -
203A ILE* 5.3 9.2 - - + -
204A GLU 3.4 9.0 - - - +
205A MET* 3.8 17.7 - - + -
534D GLU* 4.4 10.2 + - - +
538D ARG* 5.9 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 5.7 0.2 - - - +
182A ARG* 4.0 20.7 - - - +
183A ILE* 1.3 76.7 - - - +
185A TYR* 1.3 67.6 + - - +
203A ILE* 4.1 0.3 - - - -
204A GLU* 2.9 42.6 + - + +
534D GLU* 4.7 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A HIS* 4.1 33.7 + + - +
40A GLY* 4.2 16.4 - - - -
41A ASN* 4.0 20.0 - - - +
44A ARG* 3.4 46.8 + - + -
183A ILE* 5.8 2.2 - - + -
184A ALA* 1.3 80.2 - - - +
186A ASN* 1.3 69.8 + - - +
187A VAL* 5.3 1.3 - - + -
201A LEU* 3.7 18.8 - - + -
202A VAL 3.4 13.5 - - - +
203A ILE* 3.8 15.9 - - + -
204A GLU* 5.6 0.4 - - - -
1216C ARG* 5.5 1.7 - - - +
1217C THR* 4.2 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TYR* 1.3 81.0 - - - +
187A VAL* 1.3 67.1 - - - +
200A LYS 4.0 0.3 - - - +
201A LEU* 3.5 3.7 - - - +
202A VAL* 3.1 47.4 + - - +
204A GLU* 4.2 14.1 + - - +
626D TYR* 6.3 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY* 4.6 10.3 - - - -
37A HIS* 3.4 45.8 - - + +
185A TYR* 5.3 2.5 - - + -
186A ASN* 1.3 80.8 - - - +
188A GLU* 1.3 65.9 + - - +
199A ASP* 5.1 13.0 - - - +
200A LYS 3.4 9.0 - - - +
201A LEU* 3.8 22.0 - - + -
202A VAL* 6.3 0.2 - - - -
360D TYR* 5.4 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 1.3 76.1 - - - +
189A ALA* 1.3 63.5 + - - +
190A ALA 3.7 0.2 + - - -
199A ASP* 3.9 9.0 - - - +
200A LYS* 2.5 78.6 + - + +
202A VAL* 3.8 12.8 - - + +
360D TYR* 5.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU* 1.3 80.9 - - - +
190A ALA* 1.3 63.9 + - - +
198A LEU 4.4 5.6 - - - +
200A LYS* 4.3 8.8 - - - +
360D TYR* 4.8 20.5 - - + +
441D LEU 6.0 1.8 - - - +
443D GLU* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 5.2 2.5 - - + -
30A PRO* 4.8 11.2 - - + -
188A GLU 3.7 1.4 + - - -
189A ALA* 1.3 77.5 - - - +
191A ARG* 1.3 65.4 + - - +
196A THR 3.5 15.6 - - - +
198A LEU* 3.8 24.9 + - + -
199A ASP 3.7 28.0 - - - +
200A LYS* 4.0 11.4 - - + -
443D GLU* 5.0 1.2 - - - +
----------------------------------------------------------
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