Contacts of the strand formed by residues 189 - 197 (chain A) in PDB entry 1UWV
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 LEU 189 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.8 34.9 - - + +
136A ASN* 5.6 0.5 - - - -
144A LEU* 4.7 5.8 - - + -
180A LEU* 4.0 31.0 - - + +
183A LEU* 4.3 13.9 - - + -
185A ALA* 3.4 23.1 - - + +
186A MSE 3.8 21.8 + - - +
187A ARG 3.7 2.4 - - - +
188A HIS* 1.3 79.5 - - - +
190A GLY* 1.3 62.3 + - - +
205A LEU* 4.2 17.3 - - + -
206A ARG 4.1 2.2 - - - +
207A HIS* 4.0 19.7 - - + -
208A THR* 4.4 3.2 - - - +
211A LEU* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER* 4.4 1.0 - - - -
135A LEU* 3.3 25.4 + - - +
189A LEU* 1.3 72.7 - - - +
191A HIS* 1.3 67.0 + - - +
206A ARG* 2.8 22.9 + - - -
207A HIS* 4.1 1.8 - - - +
208A THR* 4.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 2.7 48.1 + - + +
133A LEU 3.4 15.7 - - - +
134A SER* 4.2 7.2 - - - -
135A LEU* 3.8 8.5 - - - +
190A GLY* 1.3 79.9 - - - +
192A VAL* 1.3 61.1 + - - +
193A GLU* 3.7 2.5 - - - -
204A ILE 4.5 0.2 - - - -
205A LEU* 3.5 4.7 - - - +
206A ARG* 2.8 69.7 + - + +
1434A NI 2.1 41.9 - - + +
1435A PO4 3.7 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ALA 4.0 0.7 - - - +
132A ARG* 3.7 0.4 - - - -
133A LEU* 2.9 62.1 + - + +
135A LEU* 4.4 4.7 - - + -
146A MSE 4.6 5.6 - - - -
176A VAL* 4.5 8.3 - - + -
180A LEU* 4.3 16.2 - - + -
191A HIS* 1.3 76.2 - - - +
193A GLU* 1.3 65.6 + - - +
194A LEU* 4.2 6.8 + - + -
203A MSE 3.9 28.5 - - + -
204A ILE 3.3 11.4 - - - +
205A LEU* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 6.5 0.2 - - + -
131A ALA 3.4 6.1 - - - +
132A ARG* 3.5 26.1 + - + -
191A HIS* 3.2 5.8 + - - -
192A VAL* 1.3 72.9 - - - +
194A LEU* 1.3 64.6 - - - +
195A VAL* 4.2 4.7 + - + -
202A LEU 3.8 0.7 - - - +
203A MSE 3.4 5.2 - - - -
204A ILE* 2.8 74.7 + - + +
206A ARG 5.3 0.2 + - - -
1434A NI 2.0 46.3 - - - +
1436A CL 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 3.2 6.2 - - - +
131A ALA* 3.0 35.4 + - + +
133A LEU* 4.1 26.7 - - + -
165A LEU* 5.5 2.9 - - + -
169A LEU* 4.0 38.9 - - + +
172A LEU* 4.6 20.0 - - + -
173A LEU* 4.7 6.7 - - + -
176A VAL* 4.4 19.1 - - + -
192A VAL* 4.4 5.2 - - + -
193A GLU* 1.3 81.4 - - - +
195A VAL* 1.3 60.6 + - - +
202A LEU 3.5 3.6 - - - +
203A MSE 3.9 24.9 - - + -
228A LEU* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 3.4 9.2 - - - +
130A ARG* 4.1 13.7 - - + -
169A LEU* 4.2 4.2 - - - +
193A GLU* 4.8 4.5 - - + -
194A LEU* 1.3 79.9 - - - +
196A GLN* 1.3 66.5 + - - +
197A ALA 4.8 0.2 - - - +
200A GLY 3.9 1.0 - - - +
201A THR* 3.4 4.0 - - - +
202A LEU* 2.8 48.8 + - + +
204A ILE* 4.3 23.8 - - + -
258A PHE* 4.4 16.2 - - + -
260A PRO 5.3 3.6 - - - +
264A ILE* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 2.8 48.9 + - + +
166A ALA* 4.7 8.7 - - + -
168A GLN* 3.1 49.4 + - + +
169A LEU* 4.0 15.4 - - + +
195A VAL* 1.3 72.8 - - - +
197A ALA* 1.3 84.4 + - - +
200A GLY* 3.7 6.1 + - - -
201A THR* 2.6 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 4.8 2.9 - - - +
195A VAL* 5.0 2.2 - - + +
196A GLN* 1.3 88.8 + - - +
198A THR* 1.3 68.2 + - - +
199A SER* 3.8 7.0 - - - +
200A GLY 3.0 24.9 + - - +
202A LEU* 5.5 1.1 - - + -
247A PRO* 5.0 1.3 - - + -
248A TRP 3.5 15.9 - - - +
249A TYR* 4.5 6.1 - - + -
258A PHE* 3.9 25.1 - - + -
----------------------------------------------------------
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