Contacts of the strand formed by residues 208 - 214 (chain A) in PDB entry 1SNG
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 TRP 208 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A THR* 3.2 6.2 - - - -
205A ALA 2.8 36.9 + - - +
206A ARG* 3.2 10.9 - - + -
207A GLY* 1.3 75.6 - - - -
209A ARG* 1.3 63.1 + - - +
224A LEU* 4.2 15.5 - - + -
225A LEU 3.4 11.4 - - - -
226A PRO* 3.6 19.7 - - + -
227A PRO* 3.5 18.6 - - + +
233A ALA* 3.7 36.4 - - + +
234A VAL 3.9 10.5 - - - -
235A PRO* 3.5 29.6 - - + -
239A LEU* 3.2 40.4 - - + +
243A LEU* 4.4 9.0 - - + -
343A HIS* 3.6 20.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 3.1 27.5 + - + -
203A ALA 3.4 7.6 - - - +
204A THR* 4.1 9.6 - - + +
207A GLY 4.3 7.4 - - - +
208A TRP* 1.3 80.0 - - - +
210A MET* 1.3 62.3 + - - +
224A LEU* 3.4 3.5 - - - +
225A LEU* 2.8 48.9 + - + +
226A PRO 6.0 0.4 - - - +
243A LEU* 4.7 0.9 - - - -
334A ILE* 3.2 16.4 - - - +
335A ARG 2.9 29.9 + - - -
336A PHE* 3.7 34.2 - - + +
337A SER 4.9 1.8 - - - +
340A ARG* 6.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 6.5 0.2 - - + -
201A PRO* 6.0 0.7 - - + +
202A TYR* 3.3 7.8 - - - -
203A ALA* 2.9 35.6 + - + +
209A ARG* 1.3 75.3 - - - +
211A VAL* 1.3 72.8 + - - +
212A THR* 3.9 16.2 - - - +
222A ASP* 3.8 22.7 - - + +
223A VAL 3.2 13.9 - - - +
224A LEU* 3.8 21.1 - - + -
240A LEU* 5.3 4.7 - - - +
243A LEU* 3.8 39.3 - - + +
244A HIS* 4.2 8.7 - - + +
247A SER* 3.5 24.0 - - - +
336A PHE* 3.7 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A MET* 3.9 14.6 - - - -
201A PRO 3.2 10.5 - - - +
202A TYR* 3.9 11.0 - - + -
210A MET* 1.3 82.8 - - - +
212A THR* 1.3 64.5 + - - +
213A LEU* 5.2 2.2 - - + -
221A VAL 3.9 0.2 - - - +
222A ASP* 3.3 3.3 - - - -
223A VAL* 2.9 42.9 + - + -
252A VAL* 4.1 17.0 - - + -
254A LEU* 4.2 15.0 - - + -
336A PHE* 3.7 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A MET* 3.8 10.0 - - - +
201A PRO* 3.1 44.0 + - + +
210A MET* 3.9 11.1 - - - +
211A VAL* 1.3 74.6 - - - +
213A LEU* 1.3 71.9 + - - +
214A HIS* 3.9 15.4 + - - +
220A ALA* 4.1 10.8 - - + -
221A VAL 3.5 5.2 - - - +
222A ASP* 2.6 26.6 + - - +
244A HIS* 5.8 0.3 + - - -
247A SER* 4.9 0.3 + - - -
347A ARG* 3.9 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TRP* 3.4 39.2 - - + -
172A PHE* 4.3 8.1 - - + -
196A ARG* 3.2 40.6 - - - +
200A MET* 4.8 2.0 - - - -
211A VAL* 4.2 3.3 - - + -
212A THR* 1.3 74.7 - - - +
214A HIS* 1.3 63.5 + - - +
215A ALA 3.8 0.3 + - - -
220A ALA* 3.6 3.3 - - - -
221A VAL* 2.8 37.9 + - + +
223A VAL* 4.4 14.8 - - + -
254A LEU* 3.9 20.4 - - + -
256A LEU* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 5.7 2.8 + - - -
168A TRP* 3.6 9.5 - - - +
169A THR* 3.0 26.2 + - - +
196A ARG* 5.4 1.8 + - - +
200A MET* 5.8 1.2 - - - +
201A PRO* 3.7 37.2 - - + +
212A THR* 3.9 11.4 + - + +
213A LEU* 1.3 76.2 - - - +
215A ALA* 1.3 61.1 + - - +
219A LEU 4.1 2.7 - - - -
220A ALA* 4.9 7.9 - - + -
503A SO4 3.4 37.4 + - - +
----------------------------------------------------------
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