Contacts of the strand formed by residues 203 - 208 (chain G) in PDB entry 6S1M
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 203 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G SER* 3.5 24.2 - - - +
135G CYS* 4.4 8.7 - - - -
160G ILE 4.3 1.1 - - - -
161G SER* 3.5 2.1 - - - -
162G CYS* 2.9 36.1 + - + +
201G GLU* 3.2 17.4 + - + +
202G PRO* 1.3 75.6 - - - +
204G GLN* 1.3 75.4 + - - +
205G LEU* 3.7 30.5 - - + -
229G MET* 4.4 9.9 - - + -
230G SER* 4.1 12.6 - - - +
231G ALA* 4.1 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G VAL* 3.9 16.6 - - + +
160G ILE 3.5 5.2 - - - -
161G SER* 3.1 22.2 + - - +
203G VAL* 1.3 80.5 - - - +
205G LEU* 1.3 73.3 + - - +
206G THR* 5.9 0.4 - - - +
231G ALA* 5.9 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G VAL 3.6 1.4 - - - +
159G VAL* 3.4 3.5 - - - -
160G ILE* 2.8 40.3 + - - +
203G VAL* 3.7 16.1 - - + +
204G GLN* 1.3 82.2 - - - +
206G THR* 1.3 61.3 + - - +
207G PHE* 3.5 28.5 - - + -
229G MET* 4.0 9.2 - - + -
230G SER 3.2 29.6 - - - +
231G ALA* 4.9 0.2 - - - -
232G ASP* 3.9 23.3 - - - +
233G VAL 4.2 4.7 - - - +
235G LEU* 5.7 0.2 - - + -
253G PRO* 4.0 21.8 - - + -
254G LYS 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G ALA* 3.9 23.6 - - + -
158G VAL 3.5 5.8 - - - +
159G VAL* 4.0 20.4 - - + +
204G GLN* 5.9 0.5 - - - +
205G LEU* 1.3 76.9 - - - +
207G PHE* 1.3 63.8 + - - +
253G PRO* 3.5 6.9 - - - +
254G LYS* 2.9 54.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G ALA* 3.2 6.1 - - - +
158G VAL* 2.7 40.0 + - - +
160G ILE* 3.5 30.7 - - + -
205G LEU* 3.5 42.0 - - + -
206G THR* 1.3 76.5 - - - +
208G ALA* 1.3 60.7 + - - +
212G LEU* 4.0 12.8 - - + -
229G MET* 5.0 1.8 - - - -
233G VAL 4.6 0.4 - - - -
235G LEU* 3.1 41.7 - - + -
251G LEU* 3.5 39.0 - - + -
252G ALA 3.9 0.9 - - - -
253G PRO* 3.5 23.8 - - + -
254G LYS* 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G VAL* 6.2 1.3 - - + -
156G ASP* 3.8 7.6 - - - +
157G ALA* 4.3 3.4 - - - +
207G PHE* 1.3 72.5 - - - +
209G LEU* 1.3 66.5 + - - +
210G ARG* 4.2 5.2 - - + +
211G TYR* 3.1 37.9 + - + +
212G LEU* 3.3 14.9 + - - +
251G LEU* 4.1 6.7 - - + +
252G ALA 5.7 0.4 + - - -
254G LYS* 4.4 15.4 - - + +
----------------------------------------------------------
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