Contacts of the strand formed by residues 186 - 191 (chain B) in PDB entry 1KLM
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 ASP 186 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 3.7 17.4 - - + +
109B LEU 3.3 10.2 - - - +
110B ASP* 4.1 4.5 - - - +
111B VAL* 4.3 0.9 - - - -
182B GLN* 3.4 12.3 - - - +
183B TYR 2.8 30.8 + - - +
185B ASP* 1.3 82.2 - - - +
187B LEU* 1.3 62.6 + - - +
188B TYR* 3.2 23.4 + - + +
408B ALA* 5.5 0.7 - - - +
409B THR* 3.3 24.1 + - - +
410B TRP* 2.8 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B THR 3.3 1.9 - - - +
108B VAL* 3.2 3.5 - - - -
109B LEU* 2.8 46.0 + - + +
111B VAL* 3.7 22.7 - - + -
164B MET* 4.2 14.4 - - + -
168B LEU* 4.2 23.8 - - + -
180B ILE* 3.8 28.3 - - + -
181B TYR 3.2 4.3 - - - +
182B GLN* 3.6 32.1 - - + -
186B ASP* 1.3 76.1 - - - +
188B TYR* 1.3 63.3 + - - +
189B VAL* 4.0 3.1 - - + +
205B LEU* 4.7 8.5 - - + -
209B LEU* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.3 14.8 - - + +
106B VAL* 3.6 17.7 - - + -
107B THR 3.1 4.9 - - - -
108B VAL* 3.4 34.3 - - + -
179B VAL 3.3 5.5 - - - +
180B ILE* 3.4 0.9 - - - -
181B TYR* 2.8 54.3 + + - +
183B TYR* 3.9 12.5 - - + +
186B ASP* 3.2 38.5 + - + +
187B LEU* 1.3 71.6 - - - +
189B VAL* 1.3 61.7 + - - +
190B GLY 3.9 0.4 + - - -
234B LEU* 5.5 0.4 - - + -
377B THR* 5.2 10.8 - - + -
380B ILE* 3.5 32.7 - - + +
381B VAL* 4.5 14.4 - - + -
410B TRP* 3.5 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER 3.8 1.7 - - - +
106B VAL* 3.2 2.5 - - - -
107B THR* 2.7 37.2 + - - +
109B LEU* 4.3 23.3 - - + -
171B PHE* 4.9 6.7 - - + -
178B ILE* 3.4 27.4 - - + -
179B VAL 3.4 1.6 - - - -
180B ILE* 3.8 21.5 - - + -
187B LEU* 4.3 8.1 - - + +
188B TYR* 1.3 73.7 - - - +
190B GLY* 1.3 58.8 + - - +
198B HIS* 3.8 7.3 - - - -
202B ILE* 3.4 28.5 - - + -
205B LEU* 4.8 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.1 4.1 - - - +
103B LYS* 3.9 16.3 - - - +
105B SER 3.3 7.9 - - - -
106B VAL* 3.6 15.9 - - - -
178B ILE* 3.3 5.2 - - - +
179B VAL* 2.8 38.6 + - - -
188B TYR 3.9 1.6 + - - -
189B VAL* 1.3 74.1 - - - +
191B SER* 1.3 60.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS* 4.0 4.2 - - - +
104B LYS* 3.6 4.0 + - - +
105B SER* 3.0 27.8 + - - +
177B ASP* 4.6 2.2 - - - -
178B ILE* 3.7 28.7 - - - -
189B VAL 4.1 0.6 + - - -
190B GLY* 1.3 73.5 - - - -
192B ASP* 1.3 66.1 + - - +
193B LEU* 3.4 19.7 + - - +
198B HIS* 2.6 35.1 + - - +
201B LYS* 6.0 0.2 - - - +
202B ILE* 6.0 0.7 - - - -
----------------------------------------------------------
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