Contacts of the strand formed by residues 335 - 340 (chain C) in PDB entry 1KXT
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 PHE 335 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 3.9 37.5 - - + -
6C THR* 4.2 6.1 - - + -
10C ARG 4.7 2.2 - - - -
11C THR* 3.4 38.8 - - + -
12C SER* 4.0 6.7 - - - -
13C ILE* 3.7 39.9 - - + -
229C PHE* 4.4 14.6 - + + -
252C ARG* 3.5 17.0 - - - +
292C ALA 3.0 15.9 + - - +
293C LEU* 3.3 12.4 - - + +
294C VAL 2.8 27.6 + - - +
334C GLY* 1.3 71.5 - - - -
336C THR* 1.3 64.0 + - - +
398C ARG* 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C THR 3.2 2.1 + - - -
12C SER* 2.7 29.8 + - - -
13C ILE 3.4 19.1 + - - -
294C VAL* 3.6 21.3 - - + -
328C MET* 3.8 29.4 - - + +
329C LEU* 3.9 4.9 - - + -
333C TYR 4.8 0.4 - - - +
335C PHE* 1.3 82.7 - - - +
337C ARG* 1.3 59.3 + - - +
338C VAL 4.2 0.2 - - - -
398C ARG* 3.2 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 3.3 25.1 - - + +
15C HIS* 4.5 13.4 - - + +
41C GLN* 2.8 43.4 + - - +
195C ARG* 3.8 1.6 - - - +
231C PHE* 3.8 13.5 - - - -
293C LEU* 4.0 15.0 - - + +
294C VAL 2.8 14.2 + - - +
295C PHE* 3.1 64.5 - - + +
296C VAL 4.7 0.9 + - - -
297C ASP 5.3 0.8 + - - -
298C ASN* 3.7 11.2 - - - +
299C HIS* 6.1 1.0 - - - -
328C MET* 3.8 6.4 - - - +
336C THR* 1.3 75.1 - - - +
338C VAL* 1.3 70.7 + - - +
339C MET* 4.0 1.9 + - + -
4004C CL 2.9 33.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER* 4.9 4.9 - - - -
13C ILE 2.8 10.8 + - - +
14C VAL* 3.2 24.8 - - + +
15C HIS* 2.8 27.5 + - - +
37C PHE* 5.3 0.2 - - + -
321C TYR* 6.0 0.4 - - - +
325C VAL* 5.0 4.3 - - + -
328C MET* 4.6 4.5 - - + -
329C LEU* 4.4 21.1 - - + -
337C ARG* 1.3 77.8 - - - +
339C MET* 1.3 71.9 + - - +
385C GLU* 5.2 1.3 - - + -
386C HIS* 4.5 9.0 - - + +
391C ILE* 4.1 21.3 - - + -
395C VAL* 4.1 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C HIS* 3.8 17.7 - - - -
17C PHE* 3.8 16.8 - - + -
297C ASP* 3.5 32.8 - - - +
298C ASN* 3.8 4.7 - - - -
299C HIS* 3.7 31.9 - - + -
302C GLN* 3.6 27.6 - - - +
321C TYR* 3.8 6.8 + - - +
337C ARG* 4.0 2.0 + - - -
338C VAL* 1.3 77.7 - - - +
340C SER* 1.3 77.7 + - - +
341C SER* 3.5 19.1 - - - +
385C GLU* 3.1 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 5.2 1.6 - - - -
15C HIS 2.9 28.5 + - - +
16C LEU* 3.8 20.2 - - - +
17C PHE* 3.5 8.4 + - - +
19C TRP* 4.5 8.3 + - - -
338C VAL 3.8 0.6 + - - -
339C MET* 1.3 81.1 - - - +
341C SER* 1.3 63.9 + - - +
384C CYS* 3.6 9.4 + - - -
385C GLU* 3.0 5.2 - - - -
386C HIS* 3.1 34.0 + - - -
----------------------------------------------------------
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