Contacts of the strand formed by residues 195 - 201 (chain G) in PDB entry 6KTR
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 TYR 195 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G LEU* 4.0 1.2 - - - +
136G LEU* 3.6 18.2 - - + -
152G TRP* 5.1 2.7 - + + -
153G LYS 3.5 3.6 - - - -
154G ALA* 3.4 24.0 - - + +
159G VAL* 5.0 1.6 - - + -
182G LEU* 3.6 24.9 - - + -
184G LEU* 3.4 29.7 - - + +
188G GLN* 2.9 30.2 + - - +
189G TRP* 3.6 31.9 - + + -
192G HIS* 3.0 29.9 + + + -
194G SER* 1.3 77.7 - - - +
196G SER* 1.3 60.3 + - - +
209G THR* 3.3 3.5 - - - -
210G VAL* 2.9 42.9 + - + +
212G PRO* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G ALA 3.5 1.7 - - - +
152G TRP* 3.4 13.0 - - - -
153G LYS* 2.8 49.2 + - - -
155G ASP 5.3 2.9 - - - -
194G SER* 5.0 3.8 - - - -
195G TYR* 1.3 75.7 - - - +
197G CYS* 1.3 58.3 + - - +
198G GLN* 3.9 2.1 - - - +
207G GLU* 2.4 40.7 + - - +
208G LYS 3.8 2.9 - - - -
209G THR* 3.3 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 197 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G VAL* 4.7 2.7 - - + +
121G LEU* 4.2 6.6 - - + +
138G CYS* 2.0 53.5 - - + -
150G VAL* 3.9 20.9 - - - -
151G ALA 3.8 2.5 - - - -
152G TRP* 3.9 15.7 - - + -
196G SER* 1.3 71.9 + - - +
198G GLN* 1.3 63.1 + - - +
199G VAL* 4.1 7.6 - - - +
206G VAL 3.9 1.0 - - - +
207G GLU* 3.5 3.3 - - - -
208G LYS 3.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G THR 3.4 1.9 - - - +
150G VAL* 3.3 4.7 - - - -
151G ALA* 2.8 52.7 + - + +
153G LYS* 4.7 20.8 - - + +
196G SER* 3.9 5.3 + - - +
197G CYS* 1.3 73.4 - - - +
199G VAL* 1.3 61.7 + - - +
200G THR* 4.8 2.3 + - - +
205G THR* 4.2 17.6 - - + +
206G VAL 3.8 4.5 - - - -
207G GLU* 2.7 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G PRO* 4.2 8.5 - - + -
119G VAL* 4.3 12.3 - - + -
140G ILE* 3.3 42.4 - - + -
148G VAL* 3.7 34.5 - - + -
149G THR 3.2 3.6 - - - +
150G VAL* 4.2 5.4 - - + -
197G CYS* 4.1 15.0 - - - -
198G GLN* 1.3 75.5 - - - +
200G THR* 1.3 63.4 + - - +
201G HIS* 3.8 0.9 + - - +
204G SER 3.8 0.7 - - - +
205G THR* 3.3 3.6 - - - +
206G VAL* 3.0 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G VAL* 3.4 7.8 - - - -
149G THR* 2.8 47.1 + - - +
151G ALA* 6.0 1.9 - - - +
198G GLN* 4.8 2.9 + - - +
199G VAL* 1.3 72.1 + - - +
201G HIS* 1.3 60.4 + - - +
202G GLU 4.2 0.6 + - - -
203G GLY* 4.3 21.1 - - - +
204G SER 3.7 4.7 - - - +
205G THR* 3.4 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 201 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G LYS* 4.1 5.8 - - + +
115G ALA 3.0 20.6 + - - -
116G ALA* 4.1 3.4 - - - +
117G PRO* 3.7 30.5 - - + +
143G PHE* 3.9 12.1 - + - -
144G TYR 3.0 27.3 + - - -
145G PRO* 3.1 24.3 + - + +
147G ALA 3.2 24.7 - - - -
148G VAL* 4.1 3.4 - - + -
199G VAL 3.8 0.4 + - - -
200G THR* 1.3 74.7 - - - +
202G GLU* 1.3 88.5 + - + +
204G SER* 2.8 27.3 + - - +
----------------------------------------------------------
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