Contacts of the strand formed by residues 188 - 193 (chain K) 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 VAL 188 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186K PRO 4.2 7.9 - - - +
187K PRO* 1.3 77.2 - - - +
189K VAL* 1.3 69.9 + - - +
190K LYS* 5.2 12.8 - - + +
240K GLU 4.1 0.5 - - - +
241K VAL* 3.4 2.6 - - - -
242K SER* 2.8 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K PRO 4.2 0.4 + - - -
188K VAL* 1.3 79.0 - - - +
190K LYS* 1.3 64.8 + - - +
191K TRP* 3.5 31.1 + - + +
209K LEU* 5.9 1.6 - - - +
211K ASP* 3.9 16.5 + - - +
222K PHE* 3.6 45.5 - - + -
239K CYS* 3.9 13.5 - - - -
240K GLU 3.4 4.7 - - - +
241K VAL* 3.6 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D ALA 5.6 2.2 + - - -
231D SER* 5.5 10.1 - - - +
232D SER 5.7 2.2 - - - +
188K VAL* 5.2 13.5 - - + +
189K VAL* 1.3 77.8 - - - +
191K TRP* 1.3 63.1 + - - +
192K PHE* 4.0 33.1 + - + -
198K ASP* 5.5 5.2 - - - +
238K ARG 4.0 0.3 - - - +
239K CYS* 3.8 1.2 - - - -
240K GLU* 2.6 60.2 + - + +
242K SER* 5.5 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 191 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161K PRO* 4.4 8.5 - - + -
174K PHE* 4.1 20.6 - - + -
175K SER* 4.5 3.6 - - - -
176K ALA* 4.5 3.6 - - + -
189K VAL* 3.5 30.3 - - + +
190K LYS* 1.3 75.8 - - - +
192K PHE* 1.3 65.1 + - - +
198K ASP* 3.4 5.0 + - - +
199K LEU* 2.9 47.2 + - + +
200K SER* 5.7 1.2 - - - +
209K LEU* 3.4 32.0 - - + +
211K ASP* 5.5 0.4 + - - -
222K PHE* 4.1 20.0 - - - +
223K GLU 4.2 4.6 + - - -
224K LEU* 3.6 30.1 - - + -
238K ARG 3.8 3.4 - - - -
239K CYS* 3.6 29.2 - - + -
252K PHE* 3.5 34.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K LYS* 4.0 31.2 - - + -
191K TRP* 1.3 85.5 - - - +
193K LYS* 1.3 58.6 + - - +
194K GLY 3.7 11.4 - - - +
195K LYS 4.4 15.0 - - - -
196K TRP 5.9 0.4 - - - -
197K VAL 3.1 14.4 - - - +
198K ASP* 3.6 28.9 - - + -
199K LEU* 4.1 5.2 - - - +
237K TYR* 3.4 6.6 - - - +
238K ARG* 2.7 61.7 + - + +
240K GLU* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 193 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192K PHE* 1.3 70.3 - - - +
194K GLY* 1.3 67.3 + - - +
197K VAL* 2.7 50.1 + - + +
199K LEU* 3.9 18.8 - - + +
202K LYS* 3.6 27.1 - - - +
232K ALA 3.0 27.2 + - - -
233K PHE* 4.2 9.6 - - - +
234K THR 4.9 7.2 + - - -
235K GLY* 5.5 2.0 - - - -
236K SER 4.3 2.2 - - - +
237K TYR* 3.4 33.7 - - + +
----------------------------------------------------------
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