Contacts of the strand formed by residues 160 - 170 (chain H) in PDB entry 1JH0
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 ILE 160 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H PRO* 4.1 24.7 - - + -
153H VAL 3.5 10.3 - - - +
154H ARG* 4.2 25.4 - - + -
158H LEU 5.5 0.7 - - - +
159H GLU* 1.3 81.8 + - - +
161H ALA* 1.3 61.8 + - - +
162H GLY 3.7 18.4 - - - +
202H ARG* 5.7 4.3 - - - +
210H SER* 4.9 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H VAL* 2.8 9.3 + - + +
155H GLY 5.2 0.2 - - - +
159H GLU 3.4 2.5 + - - +
160H ILE* 1.3 73.0 - - - +
162H GLY* 1.3 57.3 + - - +
181H VAL* 5.3 0.2 - - - -
183H LEU* 3.5 24.7 - - - +
184H LYS* 4.2 6.0 + - - +
210H SER* 4.1 13.5 - - - +
213H PHE* 3.5 50.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H PRO* 3.5 4.9 - - - +
153H VAL* 2.9 23.1 + - - +
160H ILE* 3.6 10.1 - - - +
161H ALA* 1.3 80.6 - - - +
163H LYS* 1.3 62.4 + - - +
181H VAL* 4.0 6.7 - - - -
182H GLU 3.0 14.6 - - - -
183H LEU* 4.5 3.1 - - - -
184H LYS 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H GLY* 5.2 11.8 + - - +
151H LEU 3.5 12.6 - - - +
152H PRO* 4.2 4.5 - - + -
153H VAL* 4.3 1.3 - - - +
162H GLY* 1.3 77.4 - - - +
164H VAL* 1.3 66.4 + - - +
165H VAL* 3.9 21.1 - - + -
181H VAL* 2.9 11.0 - - - +
182H GLU* 2.8 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H PRO 3.7 17.7 - - - +
149H ILE* 4.0 12.5 - - - +
150H GLY* 2.8 25.9 + - - -
151H LEU 2.9 19.9 + - - +
153H VAL* 3.8 18.8 - - + -
163H LYS* 1.3 77.5 - - - +
165H VAL* 1.3 63.7 - - - +
166H ASP 3.7 20.9 - - - +
179H LEU* 4.0 27.6 - - + -
180H GLU 3.5 7.2 - - - +
181H VAL* 4.5 2.2 - - + +
203H VAL* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H LYS* 5.0 6.3 + - - +
149H ILE* 4.1 12.2 - - - +
163H LYS* 3.9 15.7 - - + +
164H VAL* 1.3 77.9 - - - +
166H ASP* 1.3 65.9 + - + +
180H GLU* 3.0 38.7 + - + +
182H GLU* 3.6 36.3 - - + +
188H THR* 4.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 166 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H PRO* 3.3 16.8 - - - +
134H MET* 3.1 40.4 + - - +
135H LYS* 3.4 30.7 + - - +
149H ILE* 4.2 11.4 - - - +
164H VAL* 3.6 9.7 - - - +
165H VAL* 1.3 86.1 - - + +
167H ILE* 1.3 75.3 + - - +
168H TRP* 5.0 0.2 - - - -
179H LEU* 3.7 0.7 - - - -
180H GLU* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H MET* 3.0 34.0 + - + +
142H VAL* 3.9 17.9 - - + -
148H PRO* 3.4 36.8 - - + -
149H ILE* 3.6 27.4 - - + -
166H ASP* 1.3 80.4 + - - +
168H TRP* 1.3 69.8 + - - +
169H VAL* 3.5 18.1 + - + -
176H ALA* 4.3 17.9 - - + -
178H PHE 3.6 8.5 - - - +
179H LEU* 3.9 7.2 - - + -
10M VAL* 4.9 5.4 - - + -
12M VAL* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 168 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H ILE* 4.0 13.9 - - + -
132H LYS 3.4 4.9 - - - +
133H PRO* 3.7 29.3 - - + +
166H ASP* 4.5 1.3 - - - -
167H ILE* 1.3 77.0 - - - +
169H VAL* 1.3 60.6 + - - +
177H ARG* 3.2 21.7 + - - -
178H PHE* 2.9 26.1 + + + +
180H GLU* 2.6 51.9 + - + +
190H LEU* 3.5 22.8 - - + +
219H ILE* 3.7 18.2 - - + -
222H PRO 3.6 24.2 - - - -
223H THR 3.8 1.3 - - - -
224H GLU* 3.7 22.9 - - - -
225H VAL* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LYS 3.5 1.0 - - - +
131H ILE* 3.0 9.9 - - - -
132H LYS 2.8 37.7 + - - +
134H MET* 4.3 11.0 - - + -
137H ALA* 4.5 11.7 - - + -
140H PHE* 4.3 18.6 - - + -
167H ILE* 3.5 25.1 - - + +
168H TRP* 1.3 79.8 - - - +
170H ASP* 1.3 68.5 + - - +
171H ILE* 4.3 11.0 - - + +
175H MET 3.6 9.4 - - - +
176H ALA* 5.0 0.2 - - - -
177H ARG 5.1 0.4 - - - -
12M VAL* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LYS* 2.9 25.7 + - - -
131H ILE* 3.3 17.0 - - + +
169H VAL* 1.3 74.1 - - - +
171H ILE* 1.3 58.3 + - - +
172H PRO* 3.0 27.4 - - - +
173H GLU* 3.4 13.2 + - - +
174H GLN* 2.8 30.1 + - - -
175H MET* 2.9 22.8 + - + +
177H ARG* 2.8 32.1 + - - +
----------------------------------------------------------
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