Contacts of the strand formed by residues 180 - 189 (chain A) in PDB entry 1JSX
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 TYR 180 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 3.3 35.0 - - + -
149A SER* 5.6 2.2 - - - -
152A HIS* 3.3 25.4 + - + +
161A PHE* 4.0 15.9 - + - -
176A LEU* 4.7 11.7 - - + +
177A PRO* 2.8 45.8 + - + +
178A GLU* 3.1 5.6 - - - +
179A GLU* 1.3 95.0 - - + +
181A GLN* 1.3 60.8 + - - +
202A ILE* 3.9 11.7 - - + -
203A LYS 3.4 3.4 - - - +
204A ALA* 3.6 32.3 - - + -
205A ASN* 3.7 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 5.3 0.7 - - - -
180A TYR* 1.3 74.7 - - - +
182A VAL* 1.3 62.5 + - - +
183A GLU* 3.1 25.3 + - - +
202A ILE* 3.3 4.8 - - - -
203A LYS* 2.7 47.9 + - + +
204A ALA 5.0 1.2 - - - +
205A ASN* 2.8 33.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 3.6 33.0 - - + -
176A LEU* 3.8 18.6 - - + -
181A GLN* 1.3 76.3 + - - +
183A GLU* 1.3 59.6 + - - +
184A SER* 3.6 24.7 - - - +
185A VAL* 3.6 20.9 - - + -
200A VAL* 4.2 15.3 - - + -
201A VAL 3.4 6.3 - - - +
202A ILE* 4.3 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN* 5.0 3.3 + - - -
160A ARG* 2.6 37.5 + - - -
181A GLN* 3.1 22.3 + - - +
182A VAL* 1.3 73.8 - - - +
184A SER* 1.3 64.0 + - - +
201A VAL* 2.7 19.7 + - + +
203A LYS* 3.0 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 3.3 4.4 - - - +
183A GLU* 1.3 87.9 + - - +
185A VAL* 1.3 70.1 + - - +
186A VAL* 4.2 6.6 - - - +
201A VAL* 2.9 52.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A MET* 4.1 28.9 - - + -
173A ILE* 4.5 6.5 - - + -
182A VAL* 3.6 19.1 - - + -
184A SER* 1.3 81.1 - - - +
186A VAL* 1.3 63.7 + - - +
187A LYS* 3.8 2.7 + - + +
198A HIS* 3.8 31.0 - - + +
199A LEU 3.3 9.4 - - - +
200A VAL* 4.6 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 3.9 44.4 - - + +
184A SER* 4.7 11.4 - - - +
185A VAL* 1.3 76.1 - - - +
187A LYS* 1.3 63.1 + - - +
188A LEU* 3.5 18.7 + - + +
198A HIS* 3.4 4.1 - - - -
199A LEU* 2.9 57.0 + - + +
201A VAL* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 3.8 5.0 + - + +
186A VAL* 1.3 74.0 - - - +
188A LEU* 1.3 65.1 + - - +
189A GLN* 4.0 38.1 + - + +
196A GLU* 5.0 14.1 - - + -
197A ARG 3.6 4.7 - - - +
198A HIS* 3.6 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 4.1 35.0 - - + -
60A VAL* 4.7 4.0 - - + -
63A TYR* 3.7 34.3 - - + +
164A LEU* 4.6 13.0 - - + -
186A VAL* 3.9 20.2 - - + +
187A LYS* 1.3 76.2 - - - +
189A GLN* 1.3 63.8 + - - +
190A VAL* 3.9 8.3 - - + -
191A PRO* 5.3 1.3 - - + +
195A GLY 3.9 6.2 - - - +
196A GLU* 4.6 2.1 - - - +
197A ARG* 2.8 40.8 + - + +
199A LEU* 4.6 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS* 4.0 42.3 + - + +
188A LEU* 1.3 77.9 - - - +
190A VAL* 1.3 66.5 + - - +
195A GLY 4.9 2.9 - - - -
196A GLU* 6.5 0.9 - - + -
----------------------------------------------------------
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