Contacts of the strand formed by residues 279 - 286 (chain C) in PDB entry 2A19
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 GLY 279 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C SER* 3.5 0.7 - - - -
276C GLY* 3.0 31.7 + - - +
278C PHE* 1.3 80.2 - - - +
280C GLN* 1.3 72.9 + - - +
281C VAL* 5.4 1.8 - - - +
296C LYS* 5.9 3.1 - - - -
297C ARG 3.4 13.0 - - - -
298C VAL* 4.6 2.5 - - - -
334C PRO* 3.6 10.2 + - - -
2640C ANP 5.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 3.8 22.9 - - + -
274C GLY 3.5 3.1 - - - -
275C SER* 3.6 19.8 + - - +
276C GLY 4.4 1.9 - - - +
279C GLY* 1.3 82.9 - - - +
281C VAL* 1.3 64.3 + - - +
282C PHE* 3.9 12.8 - - + -
295C ILE 3.9 0.3 - - - +
296C LYS* 3.4 4.9 - - - +
297C ARG* 2.9 74.4 + - + +
333C ASP 4.9 0.2 + - - -
334C PRO* 3.1 36.9 - - - +
336C THR 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 3.6 2.8 - - - +
273C ILE* 2.9 36.6 + - + -
274C GLY* 3.0 24.5 + - - +
279C GLY 5.4 1.8 - - - +
280C GLN* 1.3 77.4 - - - +
282C PHE* 1.3 61.2 + - - +
294C VAL* 3.5 32.3 - - + -
295C ILE 3.7 3.6 - - - +
296C LYS* 4.3 18.4 - - + +
2640C ANP 3.7 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C HIS* 4.0 25.6 - + + -
258C THR* 5.7 0.2 - - - -
263C PHE* 3.8 30.5 - + + -
270C ILE* 3.6 18.6 - - + -
271C GLU 3.2 16.2 - - - +
272C LEU* 3.6 31.0 - - + -
273C ILE* 4.2 3.8 - - - -
280C GLN* 3.9 13.2 - - + -
281C VAL* 1.3 76.9 - - - +
283C LYS* 1.3 58.3 + - - +
294C VAL* 3.3 7.3 - - - +
295C ILE* 2.7 43.8 + - + +
297C ARG* 3.8 49.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C GLU* 3.5 8.6 - - - +
270C ILE* 3.4 1.2 - - - +
271C GLU* 2.8 63.1 + - - +
273C ILE* 4.0 28.1 - - + +
282C PHE* 1.3 74.6 - - - +
284C ALA* 1.3 67.5 + - - +
292C THR* 3.8 20.2 - - + -
293C TYR 3.4 6.7 - - - +
294C VAL* 5.1 0.2 - - + -
368C PHE* 3.8 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C PHE* 4.3 1.8 - - + -
267C PHE* 3.8 26.4 - - + -
268C LYS 3.4 15.5 - - - +
269C GLU* 3.9 4.3 - - - -
270C ILE* 3.8 12.8 - - + -
283C LYS* 1.3 78.2 - - - +
285C LYS* 1.3 62.3 + - - +
292C THR* 4.4 5.2 - - - -
293C TYR* 2.8 36.9 + - - +
295C ILE* 3.9 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PHE* 3.5 4.2 - - - -
268C LYS* 2.9 62.8 + - + +
269C GLU* 2.8 38.6 + - - +
284C ALA* 1.3 74.0 - - - +
286C HIS* 1.3 62.3 + - - +
290C GLY* 3.8 22.2 - - - +
291C LYS 3.2 14.6 - - - +
292C THR* 4.0 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B TYR* 4.9 0.2 - - - -
325B GLY* 5.5 1.6 - - - -
326B CYS* 3.6 37.8 + - - -
266C ASP* 3.9 21.7 + - + -
267C PHE* 4.0 21.2 - + + -
268C LYS* 4.6 4.5 + - - -
284C ALA 4.0 0.8 + - - -
285C LYS* 1.3 75.3 - - - +
287C ARG* 1.3 63.2 + - - +
288C ILE* 3.2 19.4 + - + +
289C ASP* 3.0 58.6 + - - +
290C GLY* 3.2 19.4 + - - -
291C LYS 2.7 11.9 + - - +
293C TYR* 3.8 11.6 - - + -
365C GLN* 4.5 4.6 + - - -
----------------------------------------------------------
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