Contacts of the strand formed by residues 191 - 196 (chain C) in PDB entry 1RIW
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 GLN 191 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.5 22.4 - - + +
40B GLY* 3.9 6.1 + - - +
41B SER* 3.3 22.5 + - - +
42B ASP* 3.0 26.0 + - - +
175B THR* 3.2 9.2 - - - +
176B GLY 3.1 39.5 + - - +
180B LEU* 3.9 20.0 - - + +
187C PRO* 3.7 27.6 - - + +
188C SER 5.4 0.2 - - - +
189C VAL* 3.2 18.4 + - - +
190C LEU* 1.3 77.6 + - - +
192C VAL* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 5.4 3.1 - - - +
37B ILE* 4.4 2.2 - - - -
40B GLY* 3.3 1.2 - - - -
41B SER* 2.8 49.2 + - - +
42B ASP 4.0 2.7 - - - +
43B ALA* 3.9 17.9 - - + -
47B MET* 4.2 16.8 - - + -
173B ARG* 3.4 39.9 - - + +
174B VAL 3.5 5.4 - - - -
175B THR* 3.8 10.3 - - + -
191C GLN* 1.3 76.4 - - - +
193C VAL* 1.3 69.5 + - - +
194C ASN* 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.9 23.1 - - + -
39B GLU 4.0 19.3 - - - +
40B GLY* 4.1 1.1 - - - -
173B ARG* 3.4 1.2 - - - -
174B VAL* 2.9 41.9 + - + +
192C VAL* 1.3 80.0 - - - +
194C ASN* 1.3 73.5 + - - +
195C LEU* 3.8 23.4 + - + -
227C ARG 4.5 3.6 - - - +
228C GLY* 4.0 16.4 - - - -
229C ASP 4.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.2 34.3 + - - +
27A GLU* 2.8 34.6 + - - +
28A LEU* 3.8 16.4 - - + +
171B LYS* 4.9 2.5 - - + -
172B GLY 3.2 8.3 - - - +
173B ARG* 3.1 35.1 + - - +
192C VAL* 4.5 1.4 - - - +
193C VAL* 1.3 79.4 - - - +
195C LEU* 1.3 69.5 + - - +
220C TYR* 3.8 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LYS* 3.3 4.0 - - - -
172B GLY* 2.8 34.9 + - - +
174B VAL* 4.4 6.7 - - + +
193C VAL* 3.8 22.6 + - + +
194C ASN* 1.3 82.6 - - - +
196C PRO* 1.3 69.4 - - + +
197C ILE 3.8 0.3 + - - -
218C ALA* 4.4 8.1 - - + +
219C GLY* 4.1 17.3 - - - +
220C TYR* 4.0 19.1 - - + -
227C ARG 4.1 0.7 - - - +
228C GLY* 3.4 30.1 - - - +
229C ASP* 4.0 18.2 - - - +
239C PHE* 4.0 8.7 - - + -
270C TYR* 4.1 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLY* 3.9 15.5 - - - +
170B TYR 3.3 6.7 - - - +
171B LYS* 3.8 18.1 - - + -
195C LEU* 1.3 87.8 - - + +
197C ILE* 1.3 65.2 + - - +
198C VAL* 5.4 0.4 - - + -
218C ALA* 3.2 2.3 - - - -
219C GLY 2.9 44.9 + - - +
220C TYR* 3.7 38.6 - - + +
224C GLU* 4.8 6.5 - - - +
----------------------------------------------------------
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