Contacts of the strand formed by residues 173 - 182 (chain B) in PDB entry 5I7L
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 173 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA* 5.2 2.2 - - + -
166B VAL 3.4 19.1 - - - +
167B ARG* 3.6 25.3 - - + +
172B ARG* 1.3 74.8 - - - +
174B HIS* 1.3 73.4 + - - +
236B ILE* 4.6 16.7 - - + +
239B VAL* 4.1 17.7 - - + +
240B HIS* 5.0 17.9 - - + -
243B VAL* 3.9 34.1 - - + -
247B ILE* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU 3.4 0.5 - - - +
165B ALA* 3.3 6.2 - - - +
166B VAL* 2.8 55.6 + - + +
168B ASP* 3.1 34.1 + - + -
172B ARG* 3.9 17.4 - - + +
173B ILE* 1.3 82.6 + - - +
175B LEU* 1.3 69.3 + - - +
176B VAL* 4.9 2.0 - - + -
232B ARG* 5.3 14.8 + - - +
239B VAL* 4.4 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.7 4.9 - - + -
129B LEU* 5.1 0.7 - - + -
163B ILE* 3.7 23.1 - - + -
164B LEU 3.5 1.1 - - - +
165B ALA* 4.1 15.0 - - + +
174B HIS* 1.3 78.0 - - - +
176B VAL* 1.3 60.3 + - - +
231B LEU* 3.6 27.8 + - + +
232B ARG* 4.3 3.6 + - - +
234B LEU* 4.0 29.6 - - + -
239B VAL* 4.0 16.6 - - + +
242B ILE* 4.0 30.7 - - + -
243B VAL* 3.6 27.6 - - + -
246B LEU* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 3.8 1.0 - - - -
164B LEU* 2.7 54.8 + - + +
166B VAL* 3.5 36.3 - - + -
174B HIS* 4.9 3.1 - - + -
175B LEU* 1.3 75.3 - - - +
177B LEU* 1.3 77.0 + - - +
228B ASN* 3.5 19.5 - - - +
231B LEU* 3.5 7.4 - - - +
232B ARG* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA* 3.4 31.6 - - + -
162B GLU 3.9 6.5 - - - +
163B ILE* 5.2 1.8 - - + -
164B LEU* 4.7 1.0 - - - +
176B VAL* 1.3 81.7 - - - +
178B GLY* 1.3 68.2 + - - +
180B CYS* 3.8 21.5 - - + -
224B CYS* 3.3 29.8 - - + +
227B VAL* 3.7 17.5 - - + -
228B ASN* 3.0 34.6 + - + +
231B LEU* 3.4 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLU* 2.7 20.1 + - - -
164B LEU* 3.7 23.3 - - - -
176B VAL 3.5 1.8 + - - -
177B LEU* 1.3 83.7 - - - +
179B ASP* 1.3 68.8 + - - -
180B CYS* 3.3 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B THR 3.7 2.4 - - - +
161B ALA* 3.3 3.5 - - - -
162B GLU* 3.2 38.5 + - + +
178B GLY* 1.3 70.8 - - - -
180B CYS* 1.3 59.1 + - - +
181B THR* 4.1 6.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 3.7 19.7 - - - -
160B THR 3.6 2.2 - - - -
161B ALA* 3.8 13.2 - - + -
177B LEU* 3.8 20.9 - - + -
178B GLY 3.3 3.5 + - - +
179B ASP* 1.3 73.6 - - - +
181B THR* 1.3 62.7 + - - +
220B GLN* 3.1 20.6 + - - -
224B CYS* 2.0 57.5 - - + -
227B VAL* 5.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 3.6 10.6 - - - +
160B THR* 3.0 34.7 + - - +
179B ASP* 4.1 6.1 + - + -
180B CYS* 1.3 81.6 - - - +
182B HIS* 1.3 72.0 + - - +
183B SER* 5.5 0.2 - - - -
184B PRO* 5.5 2.1 - - - +
220B GLN* 3.5 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.8 17.9 - - + -
158B ASP 3.4 10.8 - - - +
159B ILE* 3.8 11.1 - - + +
181B THR* 1.3 84.2 + - - +
183B SER* 1.3 75.4 + - - +
184B PRO* 3.1 19.8 - - + +
185B GLY 4.9 2.6 + - - -
186B SER 5.5 0.7 - - - -
187B LEU* 5.6 2.7 - - + -
216B PRO* 3.3 46.0 + - + +
217B GLU* 5.3 1.0 - - + -
220B GLN* 3.8 8.3 + - - -
----------------------------------------------------------
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