Contacts of the helix formed by residues 262 - 271 (chain K) in PDB entry 2AAZ
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 HIS 262 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K ASP* 3.6 28.0 + - - -
221K GLY* 4.1 4.0 - - - -
222K LEU* 3.8 21.5 - - + -
258K VAL* 4.1 2.9 - - + -
259K TYR* 2.9 27.0 + + + +
261K ASP* 1.3 94.3 + - - +
263K VAL* 1.3 65.5 + - - +
265K PRO* 3.2 9.9 - - - +
266K LEU* 2.9 37.2 + - + +
313K MET* 3.7 31.1 - - + +
314K LYS 2.7 29.6 + - - -
315K MET* 5.2 0.4 - - - -
316K SER 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K ILE* 4.2 25.1 - - + +
46K VAL* 5.0 8.5 - - + -
258K VAL* 4.2 14.8 - - + -
259K TYR 3.5 8.9 + - - +
260K ARG* 3.5 22.8 + - - +
262K HIS* 1.3 78.2 - - - +
264K GLU* 1.3 70.7 + - + +
266K LEU* 3.3 2.6 + - - +
267K LYS* 3.1 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 264 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260K ARG 5.0 1.0 + - - +
261K ASP 5.2 0.2 - - - -
263K VAL* 1.3 81.8 - - + +
265K PRO* 1.3 73.9 - - + +
267K LYS* 3.0 53.8 + - - +
268K THR* 3.5 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 265 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261K ASP 3.7 18.4 - - - +
262K HIS* 3.2 15.3 - - - +
264K GLU* 1.3 93.9 - - + +
266K LEU* 1.3 60.9 + - - +
268K THR* 3.3 21.2 + - - +
269K GLN 3.5 3.5 + - - -
311K ILE* 3.6 19.4 - - + +
312K ASP 3.8 24.0 - - - +
313K MET* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K TYR* 4.4 0.9 - - - +
27K ILE* 3.9 41.3 - - + -
31K ILE* 4.8 1.6 - - + -
221K GLY* 4.1 13.7 - - - -
258K VAL* 3.5 33.9 - - + -
262K HIS* 2.9 25.0 + - + +
263K VAL* 3.7 4.7 - - - +
265K PRO* 1.3 72.6 - - - +
267K LYS* 1.3 59.7 + - - +
268K THR 3.1 2.2 - - - -
269K GLN* 2.9 29.4 + - + +
270K LEU* 2.9 33.2 + - - +
313K MET* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 267 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K ILE* 4.6 17.0 - - + -
263K VAL* 3.1 34.1 + - + +
264K GLU* 3.0 43.3 + - - +
266K LEU* 1.3 76.8 - - - +
268K THR* 1.3 62.0 + - - +
270K LEU* 3.4 23.8 + - + +
271K GLU* 3.4 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 268 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264K GLU 3.5 7.8 + - - -
265K PRO* 3.3 12.4 + - - +
266K LEU 3.1 0.4 - - - -
267K LYS* 1.3 80.0 - - - +
269K GLN* 1.3 60.9 + - - +
271K GLU* 3.3 29.8 + - - +
272K ARG* 4.0 28.9 - - - +
311K ILE* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 269 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K TYR* 3.9 21.1 + - - -
24K LEU* 4.3 6.1 - - + +
27K ILE* 5.8 0.2 - - - -
66K LEU* 4.8 1.9 - - - +
68K THR* 2.7 42.6 + - - +
69K LYS* 3.7 26.6 - - - +
265K PRO 3.5 1.6 + - - -
266K LEU* 2.9 34.4 + - + +
268K THR* 1.3 76.4 - - - +
270K LEU* 1.3 57.2 + - + +
271K GLU 3.0 5.2 - - - -
272K ARG* 3.0 31.5 + - - +
311K ILE* 3.2 26.2 - - + +
313K MET* 4.3 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K LEU* 3.4 51.5 - - + +
27K ILE* 4.2 23.1 - - + -
28K ARG* 3.6 46.1 + - + +
31K ILE* 4.4 8.7 - - + -
266K LEU 2.9 18.9 + - - +
267K LYS* 3.6 19.5 - - + +
268K THR 3.3 0.4 - - - -
269K GLN* 1.3 76.4 - - + +
271K GLU* 1.3 60.6 + - + +
272K ARG 3.2 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267K LYS* 3.4 19.8 - - - +
268K THR* 3.5 21.8 + - - +
269K GLN 3.0 0.4 - - - -
270K LEU* 1.3 77.5 - - + +
272K ARG* 1.3 61.8 + - + +
273K GLU* 3.9 0.9 + - - +
----------------------------------------------------------
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