Contacts of the strand formed by residues 175 - 181 (chain A) in PDB entry 1UA4
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 175 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.4 39.9 - - + +
35A ALA* 4.0 14.6 - - + -
105A TRP* 6.0 2.0 - - + -
108A LEU* 5.4 3.8 - - + -
139A LEU* 5.2 2.9 - - + -
173A ASN* 3.8 16.3 + - + +
174A CYS* 1.3 74.0 - - - +
176A HIS* 1.3 75.4 + - - +
177A TYR* 3.8 31.4 - - + +
202A ALA* 3.1 34.6 + - - +
203A ASP* 4.0 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN* 6.2 1.1 - - + -
32A ASN* 3.3 29.8 + - + +
33A ILE 3.0 5.3 + - - -
34A ASP* 3.5 5.0 - - - +
35A ALA* 2.9 24.9 + - - -
88A GLU* 4.1 0.6 + - - -
175A ILE* 1.3 85.8 - - - +
177A TYR* 1.3 63.5 + - - +
178A ILE* 3.9 0.8 + - + -
199A ILE* 4.4 4.7 - - + -
200A GLY 3.7 7.2 - - - +
201A SER* 3.8 18.0 - - - -
202A ALA 3.8 7.4 - - - -
203A ASP* 2.5 32.3 + - - -
206A ASN* 4.3 10.7 - - + +
207A THR* 5.6 0.7 - - + -
1457A GLC 2.9 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 3.4 18.8 - - + +
97A ARG* 4.2 4.8 + - + -
100A MET* 3.6 47.1 - - + -
101A LYS* 3.4 30.9 + - - +
104A GLY 4.5 7.9 - - - -
105A TRP* 4.0 22.0 - + - -
175A ILE* 3.8 20.3 - - + +
176A HIS* 1.3 73.1 - - - +
178A ILE* 1.3 61.8 + - - +
179A TYR* 3.4 28.5 - + + +
198A PHE 3.8 0.9 - - - +
199A ILE* 3.4 4.7 - - - -
200A GLY 2.9 32.7 + - - -
202A ALA* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 3.6 39.9 - - + +
35A ALA 2.8 8.5 + - - +
36A ILE* 3.5 20.3 - - + +
37A LYS* 2.8 32.6 + - - +
176A HIS 4.1 2.5 - - - +
177A TYR* 1.3 77.7 - - - +
179A TYR* 1.3 64.0 + - - +
180A GLU* 3.6 26.3 + - + +
197A ARG* 3.8 14.8 - - + -
198A PHE 3.8 1.3 - - - -
199A ILE* 3.6 31.2 - - + -
436A VAL* 3.7 14.8 - - + -
1457A GLC 3.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 3.7 33.4 - - + -
39A LEU* 4.0 15.7 - - + -
73A LEU* 4.3 5.6 - - + -
77A ILE* 3.5 34.5 - - + -
100A MET* 3.4 42.4 + - + +
103A TRP* 3.4 29.2 - + - -
104A GLY 5.2 1.6 - - - -
177A TYR* 3.4 31.7 - + + +
178A ILE* 1.3 70.6 - - - +
180A GLU* 1.3 61.4 + - - +
181A PHE* 3.8 6.1 - - - -
197A ARG* 3.1 6.9 - - - -
198A PHE* 2.9 46.2 + + - +
200A GLY 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 3.7 25.1 - - + -
37A LYS 2.9 11.7 + - - +
38A TYR* 3.8 18.0 - - + -
39A LEU* 3.0 28.5 + - - +
178A ILE* 3.6 4.9 - - + +
179A TYR* 1.3 72.1 - - - +
181A PHE* 1.3 62.2 + - - +
182A PRO* 4.8 0.3 - - - +
196A ASN 3.5 5.6 - - - +
197A ARG* 3.6 8.2 - - - +
434A SER* 3.6 10.3 - - - -
435A THR* 2.9 33.1 + - - +
436A VAL* 2.8 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.1 9.0 - - + -
77A ILE* 4.6 1.3 - - + -
80A SER* 3.5 31.6 - - - -
81A ILE* 3.6 33.0 - - + -
84A GLY* 4.5 0.2 - - - -
179A TYR 3.8 10.1 - - - -
180A GLU* 1.3 77.5 - - - +
182A PRO* 1.3 69.8 - - + +
185A PHE* 3.8 19.7 - - + -
192A ALA* 3.8 20.0 - - + -
194A ARG 3.5 20.9 - - - -
195A GLU* 3.4 2.3 - - - +
196A ASN* 3.1 58.5 + - + +
197A ARG* 3.7 8.7 - - - -
198A PHE* 4.4 0.9 - - + -
435A THR* 5.4 0.2 - - - +
----------------------------------------------------------
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