Contacts of the strand formed by residues 194 - 198 (chain A) in PDB entry 1KCX
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 194 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASN* 2.7 20.4 + - - +
163A SER* 3.3 0.9 - - - -
164A PHE 3.1 26.0 + - - +
188A LEU* 5.8 0.2 - - - +
193A ALA* 1.3 73.4 - - - +
195A ILE* 1.3 59.7 + - - +
196A LEU* 3.6 9.6 - - + +
251A TYR* 4.5 11.0 - - + -
275A PHE* 6.5 0.2 - - + -
391A ILE* 3.7 28.7 - - + +
392A PHE* 3.7 35.4 - - + -
475A PRO* 4.0 17.3 - - + -
478A LEU* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE 3.7 3.4 - - - +
166A VAL* 5.1 2.0 - - + -
185A PHE* 3.7 64.4 - - + +
188A LEU* 3.8 31.9 - - + -
189A LYS* 4.2 5.6 - - - +
193A ALA 3.7 7.8 + - - +
194A VAL* 1.3 73.3 - - - +
196A LEU* 1.3 64.7 + - - +
197A VAL* 4.5 1.3 - - + -
248A CYS* 3.9 12.6 - - + -
249A PRO* 3.9 24.8 + - - +
250A VAL* 4.3 1.5 - - + +
251A TYR* 2.8 33.3 + - - +
478A LEU* 5.8 0.2 - - - +
479A TYR* 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL 5.3 0.4 - - - +
107A HIS* 3.8 24.0 - - + +
138A HIS* 3.8 21.1 - - + +
163A SER* 4.0 12.1 - - - -
164A PHE 2.7 18.2 + - - +
165A GLN* 3.2 11.6 - - + -
166A VAL* 3.0 26.0 + - - +
194A VAL* 3.6 30.7 - - + +
195A ILE* 1.3 74.2 - - - +
197A VAL* 1.3 68.5 + - - +
251A TYR* 3.4 23.8 - - + -
253A THR* 3.8 17.7 - - + -
277A GLU* 5.4 0.9 - - - +
392A PHE* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLN* 4.3 2.2 - - - -
166A VAL* 3.5 11.2 - - + +
168A MET* 3.5 37.0 - - + -
185A PHE* 3.9 19.3 - - + -
195A ILE* 4.5 1.6 - - + -
196A LEU* 1.3 81.1 - - - +
198A HIS* 1.3 65.1 + - - +
199A ALA* 3.5 8.7 + - + +
239A ALA* 4.5 4.0 - - + -
250A VAL* 3.9 27.8 - - + -
251A TYR 3.0 10.6 + - - +
252A ILE* 4.3 8.5 - - + -
253A THR* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 5.7 0.7 - - - -
165A GLN* 3.8 11.8 - - - +
166A VAL 3.1 5.9 + - - -
167A TYR* 3.6 38.4 - + + -
168A MET* 3.0 25.5 + - - +
169A ALA* 4.0 11.5 + - + +
170A TYR* 3.6 23.0 + + - -
197A VAL* 1.3 73.3 - - - +
199A ALA* 1.3 59.4 + - - +
200A GLU* 3.2 30.4 + - + +
253A THR* 3.9 5.2 - - - -
254A LYS* 4.2 17.4 + - - -
304A SER 3.1 25.8 + - - -
305A PRO* 4.0 9.4 - - + +
----------------------------------------------------------
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