Contacts of the strand formed by residues 162 - 173 (chain B) in PDB entry 5XOU
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 ALA 162 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 5.8 3.6 - - + -
16B LEU 3.6 12.1 - - - +
17B ARG 3.3 13.5 - - - +
18B PRO* 3.5 12.6 - - + -
19B LEU* 3.9 5.4 - - - +
157B VAL* 3.4 2.4 - - - -
158B SER* 2.7 41.2 + - - +
160B SER* 4.7 5.2 - - - +
161B GLY* 1.3 78.0 - - - +
163B PHE* 1.3 64.5 + - - +
164B LEU* 3.2 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 3.5 3.1 - - - +
16B LEU* 2.6 54.5 + - + +
17B ARG* 2.7 61.6 + - + +
19B LEU* 3.7 19.5 - - + -
23B GLU* 3.5 17.0 - - - -
67B TRP* 4.0 11.2 - + - -
113B ALA* 3.9 24.5 - - + -
116B LEU* 4.0 19.7 - - + -
155B LEU* 4.1 23.8 - - + -
156B TRP 3.5 3.8 - - - -
162B ALA* 1.3 71.5 - - - +
164B LEU* 1.3 58.7 + - - +
303B LEU* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 5.1 5.4 - - + +
14B PHE 3.6 6.7 - - - +
15B ALA* 3.8 28.7 - - + +
154B ASP 3.6 0.7 - - - +
155B LEU* 3.2 10.5 - - - +
156B TRP* 2.8 66.2 + - + +
157B VAL 4.1 0.7 - - - -
158B SER* 3.3 31.4 - - - +
162B ALA* 3.2 20.0 - - + +
163B PHE* 1.3 74.2 - - - +
165B LEU* 1.3 61.7 + - - +
309B VAL* 4.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.1 7.0 - - - -
14B PHE* 2.8 51.3 + - + +
16B LEU* 4.0 20.6 - - + +
117B LEU* 4.5 16.4 - - + -
153B LEU* 4.7 4.3 - - + -
154B ASP 3.1 24.7 - - - +
155B LEU* 3.3 14.1 - - + +
156B TRP* 4.8 0.2 - - - -
163B PHE 4.2 0.6 - - - -
164B LEU* 1.3 71.0 - - - +
166B GLU* 1.3 64.9 + - - +
167B VAL* 3.5 22.7 - - + -
294B ALA* 4.1 16.4 - - + +
297B ILE* 3.6 28.5 - - + -
298B GLY 4.9 0.4 - - - +
303B LEU* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 3.3 38.8 + - - +
13B ARG* 4.1 12.4 + - + +
152B VAL 4.5 0.7 - - - -
153B LEU* 3.3 7.0 - - - +
154B ASP* 2.9 41.4 + - + +
156B TRP* 3.5 32.8 - - + -
164B LEU 4.0 1.0 + - - -
165B LEU* 1.3 75.9 - - - +
167B VAL* 1.3 63.8 + - - +
168B ASP* 5.3 3.0 - - + +
577B GLY 5.7 0.5 - - - +
579B GLY* 3.8 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 3.0 32.3 + - - +
14B PHE* 4.4 4.7 - - + -
151B ALA* 3.7 21.8 - - + -
152B VAL 3.7 2.7 - - - -
153B LEU* 3.8 9.2 - - + -
165B LEU* 3.5 30.3 - - + -
166B GLU* 1.3 80.5 - - - +
168B ASP* 1.3 65.6 + - - +
169B PRO* 4.4 0.7 - - - -
290B THR* 3.9 29.4 - - + +
293B ILE* 3.8 18.2 - - + -
294B ALA* 4.3 14.8 - - + -
297B ILE* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 3.8 16.7 + - - +
151B ALA* 3.6 3.6 - - - -
152B VAL* 2.8 46.1 + - + +
166B GLU* 5.3 3.0 - - - +
167B VAL* 1.3 75.6 - - - +
169B PRO* 1.3 79.2 - - - +
170B ALA* 4.1 0.9 - - - +
286B ARG* 3.5 6.2 + - - -
579B GLY* 5.5 1.7 - - - -
580B ARG* 2.5 46.7 + - - +
582B TYR* 4.4 0.7 + - - -
615B ARG* 4.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLY 3.0 13.5 - - - +
151B ALA* 3.8 2.6 - - + -
167B VAL* 4.4 1.8 - - + -
168B ASP* 1.3 99.1 - - - +
170B ALA* 1.3 61.5 + - - +
171B TYR* 6.0 0.2 - - + -
281B LEU* 4.3 13.9 - - + -
286B ARG* 2.8 47.8 + - + +
289B ARG* 4.4 15.3 - - + +
290B THR* 3.2 37.5 - - - +
293B ILE* 5.0 3.1 - - + -
8E T 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 3.7 10.6 - - + +
149B GLY* 3.5 1.4 - - - -
150B GLY* 2.6 44.3 + - - +
151B ALA* 4.4 5.6 - - - +
152B VAL* 4.3 19.1 - - + -
168B ASP 4.1 5.4 - - - +
169B PRO* 1.3 77.4 - - - +
171B TYR* 1.3 71.2 + - - +
286B ARG* 5.9 0.4 - - - +
289B ARG* 5.4 0.7 + - - +
8E T 3.7 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 3.8 7.5 + - - -
138B GLU 5.9 2.2 - - - -
147B VAL* 5.1 11.2 - - + -
148B LEU 3.0 18.4 - - - +
149B GLY* 4.1 5.2 - - - -
170B ALA* 1.3 84.3 - - - +
172B ARG* 1.3 62.2 + - - +
173B ILE 4.4 0.2 - - - -
279B LEU* 4.2 24.0 - - + -
281B LEU* 3.1 31.9 - - + +
286B ARG* 5.5 2.0 - - - -
289B ARG* 2.2 51.4 + - - -
7E A 5.3 0.9 - - - -
8E T 3.2 39.7 + - - +
9E G 4.0 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B TRP* 5.2 3.8 - - - +
130B GLU* 6.0 1.3 - - - +
135B TYR* 3.4 40.2 - - + +
147B VAL* 3.8 2.8 - - - -
148B LEU* 2.7 44.8 + - + +
171B TYR* 1.3 73.9 - - - +
173B ILE* 1.3 61.4 + - - +
174B LEU* 3.8 3.8 + - + +
8E T 6.0 0.2 - - - -
9E G 3.5 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG 4.7 4.5 - - - -
147B VAL* 5.7 0.4 - - - +
172B ARG* 1.3 71.9 - - - +
174B LEU* 1.3 59.6 + - - +
175B CYS* 3.9 3.1 - - + +
8E T 4.0 5.7 + - - +
9E G 2.7 35.5 + - - +
----------------------------------------------------------
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