Contacts of the strand formed by residues 197 - 200 (chain A) in PDB entry 3ZS4
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 VAL 197 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PHE* 3.3 8.7 - - + -
169A VAL* 3.8 25.1 - - + -
186A LEU* 4.3 15.9 - - + +
189A VAL* 3.8 24.5 - - + -
190A ALA* 4.0 18.2 - - + -
193A THR* 4.3 4.7 - - + -
195A ALA 4.0 7.0 - - - +
196A PRO* 1.3 77.6 - - - +
198A ILE* 1.3 69.7 + - - +
199A ALA 4.4 0.2 - - - +
219A GLY 2.8 14.5 + - - +
220A VAL* 3.4 16.2 - - + +
221A GLU* 2.8 28.4 + - - -
222A GLY 3.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 5.9 1.6 - - + -
7A LEU* 4.0 10.1 - - + -
79A GLU* 4.9 1.6 - - - +
100A ARG* 3.9 17.7 - - - +
166A ARG* 4.0 17.7 - - + -
167A PHE 2.7 13.8 + - - +
168A VAL* 3.3 13.6 - - + +
169A VAL* 2.8 31.4 + - - -
197A VAL* 1.3 76.2 - - - +
199A ALA* 1.3 59.2 + - - +
200A SER 3.7 0.2 + - - -
221A GLU* 3.4 26.0 - - + +
222A GLY* 3.4 30.5 - - - +
224A ILE* 3.7 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PRO* 6.0 0.2 - - + -
186A LEU* 3.6 40.6 - - + -
197A VAL* 4.0 2.2 + - - +
198A ILE* 1.3 74.3 - - - +
200A SER* 1.3 56.9 + - - +
212A ILE* 4.2 21.5 - - + -
220A VAL* 4.3 2.2 - - + +
222A GLY 2.8 14.8 + - - +
223A ALA* 3.3 3.3 - - - -
224A ILE* 2.7 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 4.2 5.8 - - - -
169A VAL 2.9 10.0 + - - +
170A THR* 3.3 42.4 + - - +
171A ASP 3.9 3.5 + - - -
175A ASP* 4.6 0.5 + - - -
186A LEU* 4.9 0.4 - - - +
199A ALA* 1.3 76.5 - - - +
201A GLY* 1.3 61.9 + - - +
224A ILE* 3.8 24.4 - - - +
1246A 1PR 2.6 33.4 + - - -
----------------------------------------------------------
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