Contacts of the strand formed by residues 279 - 284 (chain A) in PDB entry 1P22
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 LYS 279 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ASP* 2.7 45.6 + - - +
278A GLN* 1.3 85.1 + - - +
280A ILE* 1.3 63.1 + - - +
281A VAL* 3.7 18.6 - - + -
291A ILE* 4.1 12.8 - - + -
292A TRP 3.1 12.8 - - - +
294A LYS* 3.7 3.3 - - - +
300A LYS* 3.7 18.6 - - - +
315A TYR* 2.8 45.5 + - - +
317A GLU* 5.2 4.9 + - - -
334A VAL* 3.9 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 3.9 17.3 - - + -
273A LEU* 4.1 23.8 - - + -
274A GLN 3.6 10.5 - - - +
275A TYR* 4.8 8.7 - - + -
279A LYS* 1.3 78.9 - - - +
281A VAL* 1.3 66.3 - - - +
290A LYS 3.5 3.6 - - - +
291A ILE* 3.2 7.4 - - - -
292A TRP* 2.9 42.9 + - + +
294A LYS* 4.4 19.7 - - + -
297A LEU* 5.2 0.2 - - + -
533A VAL* 5.6 1.3 - - + -
541A ILE* 4.1 20.9 - - + -
543A ILE* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 3.3 2.9 - - - -
274A GLN* 2.8 34.3 + - + -
279A LYS* 3.7 20.4 - - + -
280A ILE* 1.3 71.4 - - - +
282A SER* 1.3 57.9 + - - +
289A ILE* 3.9 7.6 - - + -
290A LYS 4.1 2.0 - - - -
291A ILE* 4.0 11.2 - - + -
313A LEU* 3.5 24.4 - - + +
315A TYR* 3.2 31.4 - - + -
320A ILE* 3.7 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 3.8 14.1 - - - -
272A CYS 3.6 6.1 - - - -
273A LEU* 4.6 3.1 - - - -
280A ILE* 4.8 0.4 - - - -
281A VAL* 1.3 73.6 - - - +
283A GLY* 1.3 60.2 + - - +
284A LEU* 3.5 5.2 + - - +
289A ILE* 3.0 9.5 - - - +
290A LYS* 2.5 60.8 + - - +
292A TRP* 3.0 16.3 + - - -
541A ILE* 3.6 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 3.6 1.3 - - - -
271A TYR 2.8 26.9 + - - -
272A CYS* 3.0 17.0 + - - -
282A SER* 1.3 69.6 - - - +
284A LEU* 1.3 67.0 + - - +
289A ILE* 4.0 3.8 - - - -
310A VAL* 3.5 33.8 - - - +
313A LEU* 3.5 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A CYS* 4.0 23.6 - - + -
264A SER* 4.2 7.4 - - - +
267A SER* 5.2 1.8 - - - +
269A GLY 3.3 7.0 - - - +
270A VAL* 3.7 27.4 - - + +
271A TYR* 4.6 0.9 - - - -
282A SER* 4.1 12.8 - - - +
283A GLY* 1.3 78.0 - - - +
285A ARG* 1.3 62.3 + - - +
286A ASP* 3.2 30.5 - - + +
287A ASN 4.0 1.9 + - - -
288A THR 3.0 13.1 + - - +
290A LYS* 3.2 42.4 - - + -
310A VAL* 3.2 24.6 + - - +
539A ASP* 5.1 4.0 - - - +
----------------------------------------------------------
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