Contacts of the strand formed by residues 270 - 276 (chain C) in PDB entry 3KYS
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 270 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 4.9 0.7 - - + -
258C LEU* 4.6 12.3 - - + -
261C LEU* 3.4 39.3 - - + -
262C PHE* 3.6 34.8 - + + -
265C GLY* 4.2 5.6 - - - -
266C PRO 3.1 27.4 - - - -
267C GLN 3.5 10.2 + - - +
268C ASN 3.4 1.9 - - - -
269C ALA* 1.3 84.2 - - + +
271C PHE* 1.3 69.6 + - - +
384C THR* 4.2 14.1 - - + -
387C CYS* 3.4 33.0 - - + -
407C ARG* 4.1 2.9 - - - +
408C LEU* 3.2 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ARG* 6.0 1.1 - - - -
196C ILE* 3.5 25.1 - - + -
197C GLY* 3.7 40.4 - - - -
239C LEU* 4.0 19.7 - - + -
268C ASN 3.8 20.6 - - - -
269C ALA 3.7 12.1 - - - -
270C PHE* 1.3 79.6 - - - +
272C LEU* 1.3 61.0 + - - +
386C LEU* 5.1 3.4 - - + -
387C CYS* 2.9 12.1 + - - +
388C MET* 3.5 8.0 - - + -
389C ALA 2.8 26.0 + - - -
405C ILE* 4.0 13.2 - - + -
406C TYR 3.3 16.6 - - - +
407C ARG* 4.2 22.7 - - - -
408C LEU* 3.5 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C VAL* 3.8 29.8 - - + -
247C ILE* 4.2 21.8 - - + -
251C PHE* 5.1 0.2 - - + -
271C PHE* 1.3 74.5 - - - +
273C VAL* 1.3 61.3 + - - +
389C ALA* 3.3 24.9 - - + +
391C VAL* 3.9 26.0 - - + -
405C ILE* 3.7 0.2 - - - -
406C TYR* 2.7 49.2 + - + +
408C LEU* 3.8 17.6 - - + +
91D LEU* 4.7 0.9 - - + -
95D PHE* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 4.1 5.8 - - + -
227C ILE* 4.5 3.4 - - + -
271C PHE* 4.9 0.7 - - + -
272C LEU* 1.3 81.0 - - - +
274C LYS* 1.3 63.4 + - - +
275C PHE* 3.5 39.8 + - + -
388C MET* 3.6 31.9 - - + -
389C ALA 2.8 12.2 + - - +
390C CYS* 3.5 2.1 - - - -
391C VAL* 3.0 27.7 + - - +
403C HIS* 4.5 6.7 - - + -
404C HIS 3.3 9.9 - - - +
405C ILE* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU 4.2 0.8 + - - -
273C VAL* 1.3 71.4 - - - +
275C PHE* 1.3 66.7 + - - +
276C TRP* 3.5 27.5 - - + -
391C VAL* 3.5 23.6 - - + +
392C PHE 4.3 0.7 - - - -
393C GLU* 3.0 55.2 + - - +
403C HIS* 3.3 4.0 - - - -
404C HIS* 2.8 45.8 + - + +
406C TYR* 4.3 1.4 - - + -
95D PHE* 2.9 60.0 + - + +
96D PHE* 4.0 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C PHE* 4.7 9.9 - + - -
225C VAL* 3.6 37.9 - - + -
226C HIS 4.8 1.8 - - - -
227C ILE* 3.6 33.7 - - + -
273C VAL* 3.5 26.9 - - + -
274C LYS* 1.3 76.2 - - - +
276C TRP* 1.3 62.5 + - - +
277C ALA 3.8 0.2 + - - -
344C P1L 5.6 0.4 - - + -
388C MET* 5.3 1.1 - - - -
390C CYS* 4.0 24.7 - - + -
391C VAL 2.7 12.9 + - - -
392C PHE* 3.3 41.2 - + + -
393C GLU 2.9 26.5 + - - +
402C GLN 3.6 2.5 - - - -
403C HIS* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C PHE 4.4 0.5 - - - +
225C VAL* 4.7 1.2 - - - +
274C LYS* 3.5 33.7 - - + -
275C PHE* 1.3 72.5 - - - +
277C ALA* 1.3 65.4 + - - +
278C ASP 3.8 0.9 + - - -
393C GLU* 3.1 35.6 + - + +
394C VAL 4.3 1.8 - - - -
395C SER* 3.6 26.9 - - - +
396C ASN 5.1 1.3 - - - -
401C ALA* 4.1 6.2 - - - +
402C GLN* 2.7 62.4 + - + +
404C HIS* 3.4 34.8 - + + -
94D SER 3.9 1.6 - - - -
95D PHE 3.6 22.4 - - - -
96D PHE* 4.1 3.7 + - - -
97D LYS 4.1 0.2 - - - -
98D PRO* 3.6 45.6 - - + +
99D PRO* 4.2 2.7 - - + -
----------------------------------------------------------
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