Contacts of the strand formed by residues 190 - 195 (chain A) in PDB entry 5KJH
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 LEU 190 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 2.8 32.9 + - - +
157A ALA* 3.8 15.2 - - + +
158A SER 3.2 16.8 + - - +
161A THR 3.4 24.0 - - - +
162A THR* 3.5 13.5 - - - +
163A ILE* 3.5 31.6 - - + -
186A HIS* 3.4 47.3 - - + +
188A TYR 4.1 5.2 - - - +
189A ASP* 1.3 70.9 - - - +
191A LEU* 1.3 56.0 + - - +
192A SER 5.2 0.4 - - - +
205A ALA 3.7 15.9 - - - +
206A GLY* 4.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 4.1 18.3 - - - +
143A ASP* 3.5 19.0 - - - +
157A ALA* 4.8 0.2 - - - -
189A ASP* 5.2 0.4 - - + -
190A LEU* 1.3 78.9 - - - +
192A SER* 1.3 61.3 + - - +
205A ALA 2.9 5.1 + - - -
206A GLY* 3.9 7.4 - - - -
207A HIS* 3.6 35.0 - - + +
244A LEU* 3.7 24.5 - - + -
245A VAL 3.6 25.1 - - - +
246A ASP* 3.9 18.8 - - + +
327A PHE* 4.1 8.5 - - + -
328A PHE* 3.8 27.5 - - + -
330A ARG* 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASP* 3.5 9.1 + - - -
157A ALA* 4.3 5.4 - - - +
190A LEU* 3.8 0.8 - - - +
191A LEU* 1.3 80.4 - - - +
193A VAL* 1.3 64.7 + - - +
204A SER* 3.3 5.0 - - - -
205A ALA* 3.0 32.6 + - - +
246A ASP 3.7 16.2 - - - -
247A CYS* 3.6 4.0 - - - -
248A VAL* 2.8 46.5 + - - +
330A ARG* 6.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASP* 3.1 38.9 + - - +
144A LEU 4.3 1.3 - - - +
145A ALA* 3.8 13.8 - - + +
155A ALA* 3.9 36.3 - - + +
157A ALA* 4.0 8.7 - - + +
163A ILE* 3.7 25.1 - - + -
192A SER* 1.3 77.2 + - - +
194A ALA* 1.3 66.0 + - - +
195A PHE* 5.9 0.2 - - + -
202A VAL* 3.7 18.6 - - + -
203A LEU 3.2 11.2 - - - +
248A VAL 4.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA* 4.5 5.4 - - - -
193A VAL* 1.3 77.3 - - - +
195A PHE* 1.3 67.0 + - - +
196A HIS 4.2 0.2 + - - -
202A VAL* 3.3 5.0 - - - +
203A LEU* 2.8 40.8 + - + +
248A VAL* 3.4 27.4 - - + +
249A ALA* 3.9 15.7 - - + -
250A PHE* 4.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA* 3.3 31.8 - - + +
146A THR 3.7 7.4 - - - +
147A SER* 3.7 28.9 - - - -
148A PRO* 3.5 23.2 - - + +
153A ILE* 3.7 22.7 - - + -
154A ILE 4.4 0.2 - - - -
155A ALA* 3.6 24.2 - - + -
165A ILE* 4.4 4.9 - - + -
194A ALA* 1.3 78.3 - - - +
196A HIS* 1.3 60.4 + - - +
197A ASP* 4.0 0.7 + - - +
199A GLY* 3.9 16.6 - - - -
201A TYR 3.5 4.9 - - - -
202A VAL* 3.7 23.1 - - + -
216A LEU* 3.8 14.8 - - + -
250A PHE* 3.7 11.5 + - - +
----------------------------------------------------------
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