Contacts of the strand formed by residues 172 - 179 (chain G) in PDB entry 6G2T
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 ILE 172 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164G GLY* 3.5 15.9 - - - -
165G GLU 3.5 42.2 - - - +
166G VAL* 4.0 15.9 - - + -
170G GLY 4.4 0.2 + - - -
171G SER* 1.3 74.3 - - - +
173G THR* 1.3 67.9 + - - +
174G PHE* 3.6 21.4 + - + -
224G LEU 4.0 0.7 - - - +
226G ILE* 2.8 53.8 + - + +
254G LEU* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 173 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G SER* 5.5 1.2 - - - -
172G ILE* 1.3 78.6 - - - +
174G PHE* 1.3 78.2 + - - +
175G SER* 4.4 2.0 + - - -
223G GLU* 4.5 13.5 - - + -
224G LEU 3.5 6.5 - - - +
225G HIS* 3.1 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G PRO* 5.3 4.0 - - + -
162G GLN 3.0 31.0 - - - -
164G GLY* 3.5 21.3 - - - -
172G ILE* 3.6 30.1 - - + -
173G THR* 1.3 83.2 - - - +
175G SER* 1.3 59.8 + - - +
191G TRP* 4.2 5.2 - - + -
223G GLU* 3.5 2.4 - - - +
224G LEU* 2.7 57.5 + - + +
226G ILE* 4.5 5.4 - - + -
252G PHE* 3.5 34.3 - + + -
253G ASN 4.5 4.3 - - - -
254G LEU* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G MET* 4.5 13.4 - - - +
160G ARG 4.2 2.8 - - - +
161G PRO* 3.6 21.5 - - - +
162G GLN 4.9 1.1 + - - +
173G THR* 4.4 2.7 + - - -
174G PHE* 1.3 76.2 - - - +
176G ALA* 1.3 61.3 + - - +
191G TRP* 4.6 4.7 - - - -
221G LEU* 3.8 15.5 - - - +
222G PHE 3.1 12.6 - - - -
223G GLU* 3.7 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G PHE* 4.6 12.6 - - + -
159G MET* 3.6 12.6 - - - +
161G PRO* 4.1 18.2 - - + -
175G SER* 1.3 76.4 - - - +
177G ARG* 1.3 64.2 + - - +
178G VAL 4.2 0.2 + - - -
191G TRP* 4.6 3.1 - - + -
220G TYR 3.6 1.2 - - - +
221G LEU* 3.7 1.9 - - - -
222G PHE* 2.9 41.1 + - + +
239G CYS* 4.3 16.4 - - - -
241G VAL* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G PHE* 3.3 7.8 - - - -
158G VAL* 2.7 45.8 + - + +
159G MET* 3.2 43.6 + - + +
176G ALA* 1.3 71.6 - - - +
178G VAL* 1.3 59.2 + - - +
217G SER* 4.7 8.7 + - - -
219G VAL* 3.5 32.8 - - + +
220G TYR 3.3 3.6 - - - +
221G LEU* 3.7 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G LEU* 3.2 30.3 - - + +
157G PHE* 4.0 10.3 - - + -
176G ALA 5.0 0.7 - - - +
177G ARG* 1.3 78.7 - - - +
179G ALA* 1.3 70.8 + - - +
180G GLY 3.6 0.5 + - - -
187G PRO* 3.7 29.4 - - + -
219G VAL* 3.6 3.7 - - - -
220G TYR* 2.8 43.4 + - + +
222G PHE* 3.8 14.8 - - + -
241G VAL* 3.6 25.6 - - + -
243G THR* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G LEU* 3.9 6.8 + - - +
158G VAL* 3.6 26.2 - - + +
178G VAL* 1.3 81.9 - - - +
180G GLY* 1.3 65.9 + - - +
187G PRO* 5.7 0.2 - - - +
218G LYS 3.8 7.4 - - - +
219G VAL* 4.6 4.5 - - + +
220G TYR* 4.8 0.2 - - - -
243G THR* 5.7 1.6 - - - +
----------------------------------------------------------
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