Contacts of the strand formed by residues 168 - 172 (chain A) in PDB entry 3RS9
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 168 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 3.9 20.2 - - - +
31A MET* 4.1 7.0 - - + +
34A GLU* 3.9 34.5 - - + -
35A LEU* 6.5 0.2 - - + -
142A VAL* 6.3 0.4 - - + -
143A VAL 3.2 1.9 + - - +
144A VAL* 3.1 31.8 - - + +
145A SER 2.8 24.3 + - - -
166A ALA* 3.7 1.4 - - - +
167A ASP* 1.3 82.7 - - + +
169A THR* 1.3 65.5 + - - +
170A VAL* 4.2 10.5 - - + -
188A THR 3.9 0.2 - - - -
190A LYS* 3.4 23.1 - - + +
192A LYS* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER* 3.4 10.3 - - - +
147A ASP 3.4 27.8 - - - +
148A VAL* 4.0 6.7 - - - -
149A PRO* 3.7 5.8 - - + +
166A ALA* 3.6 10.0 - - - +
168A LEU* 1.3 73.0 - - - +
170A VAL* 1.3 65.7 + - - +
179A HIS* 3.8 15.0 - - + +
188A THR* 2.7 39.6 + - - -
190A LYS 2.8 7.3 + - - +
191A LEU* 3.4 7.9 - - + +
192A LYS 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 4.3 8.3 - - - +
27A VAL* 3.9 38.6 - - + +
30A ALA* 3.5 28.0 - - + -
144A VAL* 4.6 3.4 - - + -
145A SER 3.0 7.2 + - - +
147A ASP* 2.7 30.0 + - - -
168A LEU* 4.2 15.5 - - + -
169A THR* 1.3 76.2 - - - +
171A THR* 1.3 58.2 + - - +
172A PHE* 3.6 16.1 - - + -
192A LYS* 3.5 10.3 - - + +
194A ALA* 4.4 2.2 - - + -
6B PHE* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 2.5 40.3 + - - +
169A THR 4.0 0.8 - - - -
170A VAL* 1.3 72.8 - - - +
172A PHE* 1.3 71.2 + - - +
174A VAL 3.6 15.5 - - - +
175A PRO* 4.2 0.4 - - + -
176A LYS* 2.9 10.2 + - - -
179A HIS* 3.3 23.1 - - + +
191A LEU* 3.9 5.2 - - + -
192A LYS 2.9 9.9 + - - +
193A VAL* 3.8 23.6 - - + -
194A ALA* 2.9 24.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
1A MET* 4.0 8.2 - - - +
23A ALA* 3.6 32.1 - - + -
26A SER* 4.5 1.3 - - - -
27A VAL* 4.0 3.1 - - + -
55A ASP* 3.7 17.7 - - - -
146A VAL* 3.9 14.1 - - + -
147A ASP* 3.8 30.7 - - + +
170A VAL* 3.6 28.9 - - + -
171A THR* 1.3 87.1 + - - +
173A GLY* 1.3 62.6 + - - +
174A VAL 2.9 3.3 + - - -
176A LYS* 2.8 24.5 + - - +
193A VAL* 4.7 0.2 - - - -
194A ALA* 3.5 5.4 - - + -
196A ILE* 3.6 39.0 - - + -
198A HIS* 4.9 2.9 - - + -
495A GOL 4.1 17.9 - - - +
----------------------------------------------------------
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