Contacts of the strand formed by residues 171 - 178 (chain A) in PDB entry 1XV2
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 GLY 171 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE 3.4 1.7 - - - +
159A PHE* 3.3 28.8 - - - -
160A THR* 2.9 32.7 + - - -
165A HIS* 3.5 3.9 + - - -
169A SER* 2.8 12.5 + - - +
170A ALA* 1.3 72.6 - - - +
172A PHE* 1.3 63.6 + - - -
173A HIS 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 3.5 62.8 - + + -
99A ILE* 3.7 40.4 - - + -
100A LYS* 4.0 13.2 - - + -
103A MSE 3.7 13.9 - - + -
112A VAL* 4.3 16.2 - - + -
158A PHE 3.5 4.5 - - - -
159A PHE* 3.7 32.3 - + + -
169A SER* 4.3 3.5 + - - -
170A ALA 3.9 3.9 + - - +
171A GLY* 1.3 73.0 - - - -
173A HIS* 1.3 60.5 + - - +
174A ILE* 4.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.2 0.9 - - + +
36A ILE* 3.4 29.8 - - + +
73A TYR* 4.7 22.9 + + - -
75A SER* 6.0 0.2 + - - -
157A GLY* 2.9 3.8 - - - -
158A PHE* 2.9 37.2 + - + +
160A THR* 5.9 0.2 - - - +
169A SER* 3.0 25.8 + - - +
172A PHE* 1.3 72.4 - - - +
174A ILE* 1.3 62.5 + - - +
175A HIS* 4.1 1.6 - - - -
186A HIS* 3.2 21.8 - + - -
234A GLU* 3.1 23.1 + - - +
801A ZN 2.3 30.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 4.9 0.4 - - - -
92A GLN* 4.5 0.4 - - - +
96A PHE* 3.8 31.2 - - + -
112A VAL* 4.1 14.6 - - + -
114A ILE* 5.6 1.1 - - + -
155A ILE* 3.5 29.2 - - + -
156A VAL 3.2 2.9 - - - -
157A GLY* 3.6 15.7 - - - +
172A PHE* 4.9 6.5 - - + -
173A HIS* 1.3 87.0 - - - +
175A HIS* 1.3 70.0 + - - +
186A HIS* 3.8 3.9 + - - -
187A VAL* 2.9 53.0 + - + +
190A PHE* 3.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 3.4 24.8 - - + +
37A ALA 3.4 21.3 - - - -
45A GLU* 3.4 17.8 + - - +
46A VAL 2.9 22.0 + - - -
47A ILE* 3.6 17.8 - - + +
154A ALA 4.0 0.2 - - - +
155A ILE* 3.2 4.5 - - - +
156A VAL* 2.8 33.2 + - - +
173A HIS* 3.5 4.6 + + - -
174A ILE* 1.3 86.0 - - - +
176A PHE* 1.3 61.5 + - - +
185A GLY 3.1 9.4 - - - +
186A HIS* 3.4 11.0 + - - -
187A VAL* 3.9 3.4 - - - -
801A ZN 2.3 35.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 3.7 9.4 - - - +
118A PHE* 3.6 14.8 - + - -
121A MSE 3.4 24.5 - - + -
123A VAL* 4.3 3.1 - - + -
151A ILE* 4.0 17.0 - - + -
153A GLY* 3.6 23.3 - - - -
154A ALA 3.2 38.4 - - - -
155A ILE* 3.6 3.8 - - + -
175A HIS* 1.3 75.4 - - - +
177A ALA* 1.3 69.3 + - - +
178A ASP* 3.5 20.9 - - + -
183A TYR* 3.8 34.8 - + - -
184A GLY* 3.1 4.5 - - - -
185A GLY 2.8 31.7 + - - +
187A VAL* 3.6 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 4.2 20.2 - - + -
49A LEU* 4.4 7.2 - - + -
54A TYR* 5.1 2.9 - - + -
62A PHE* 4.0 18.8 - - + -
154A ALA* 2.9 28.6 + - - +
176A PHE* 1.3 80.3 - - - +
178A ASP* 1.3 64.1 + - - +
181A ARG* 3.4 19.2 + - - +
183A TYR 3.7 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 5.1 0.4 - - - -
148A ARG* 4.8 2.3 + - - -
151A ILE* 3.5 30.1 - - + +
152A ARG 3.5 10.1 - - - +
153A GLY* 3.7 2.5 - - - -
176A PHE* 3.5 5.6 - - + -
177A ALA* 1.3 72.6 - - - +
179A ASP* 1.3 55.2 + - - +
180A GLU* 3.3 28.3 + - - +
181A ARG* 2.7 36.5 + - - -
182A ALA* 2.8 24.5 + - - +
183A TYR* 3.0 28.9 + - - +
----------------------------------------------------------
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