Contacts of the helix formed by residues 278 - 287 (chain A) in PDB entry 2N5T
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 VAL 278 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A THR* 1.3 73.5 - - + +
279A ARG* 1.3 84.9 + - + +
281A VAL* 2.8 41.1 + - + +
282A GLU* 4.1 1.6 + - - +
316A ALA* 4.3 2.9 - - - +
319A ALA* 3.6 32.8 - - + +
320A VAL* 3.6 27.3 - - + +
323A ALA* 5.0 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A THR* 2.6 33.5 + - + +
278A VAL* 1.3 90.0 - - + +
280A ASP* 1.3 62.0 + - - +
281A VAL 3.3 0.6 + - - -
282A GLU* 3.7 21.9 - - - +
283A GLY 4.4 0.9 + - - -
303A ASP* 2.9 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASN 5.1 0.9 - - - +
275A ILE* 3.3 23.1 - - + +
276A GLY* 2.7 28.4 + - - -
277A THR* 2.6 26.9 + - - +
279A ARG* 1.3 74.5 - - - +
281A VAL* 1.3 62.5 + - - +
282A GLU 3.1 2.6 + - - -
283A GLY* 3.3 4.9 + - - +
284A ALA* 3.0 20.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
275A ILE* 4.3 15.5 - - + -
278A VAL* 2.8 29.6 + - - +
280A ASP* 1.3 76.2 - - - +
282A GLU* 1.3 65.2 + - - +
284A ALA* 3.5 7.9 - - + +
285A GLU* 2.9 37.0 + - + +
292A VAL* 5.4 0.7 - - + -
320A VAL* 4.6 2.7 - - + -
323A ALA* 3.1 39.7 - - + +
324A CYS* 3.8 25.1 - - - -
327A GLN* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A VAL 4.1 1.0 + - - +
279A ARG* 3.7 16.0 + - - +
281A VAL* 1.3 82.4 - - - +
283A GLY* 1.3 58.0 + - - +
285A GLU* 3.0 9.4 + - - +
286A ARG* 2.8 57.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
279A ARG 4.4 1.2 + - - -
280A ASP* 3.3 8.9 + - - +
282A GLU* 1.3 76.5 - - - +
284A ALA* 1.3 60.1 + - - +
286A ARG* 3.3 21.2 + - - +
287A ASN* 2.5 38.1 + - - -
527A ALA* 3.6 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 3.5 25.8 - - + -
275A ILE* 4.8 2.9 - - + -
280A ASP 3.0 13.6 + - - +
281A VAL* 3.5 13.2 - - + +
282A GLU 3.1 0.4 - - - -
283A GLY* 1.3 76.7 - - - +
285A GLU* 1.3 63.8 + - + +
287A ASN* 3.4 1.4 + - - +
288A GLY 3.2 3.8 + - - -
289A ALA* 2.9 37.1 + - + +
291A GLY 5.5 0.2 - - - +
292A VAL* 5.3 5.6 - - + -
527A ALA* 3.8 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 2.9 28.7 + - + +
282A GLU* 3.7 7.4 - - - +
284A ALA* 1.3 77.8 - - + +
286A ARG* 1.3 64.2 + - - +
287A ASN 3.2 0.5 + - - -
288A GLY* 3.3 11.8 + - - -
289A ALA* 5.0 3.8 - - - +
323A ALA 3.0 23.6 - - - +
324A CYS* 4.6 3.8 - - - -
327A GLN* 4.6 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ALA* 4.7 12.1 - - - +
282A GLU* 2.8 50.0 + - - +
283A GLY* 3.3 35.9 - - - +
285A GLU* 1.3 79.4 - - - +
287A ASN* 1.3 65.7 + - - +
288A GLY 3.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLY* 2.5 31.7 + - - +
284A ALA 4.2 1.1 - - - +
285A GLU 3.2 0.2 - - - -
286A ARG* 1.3 85.1 - - - +
288A GLY* 1.3 58.8 + - - +
289A ALA 3.4 1.6 - - - -
527A ALA* 3.3 38.9 - - + +
528A ILE* 3.9 16.4 - - - +
530A ILE* 3.1 23.4 - - + +
531A PRO* 3.8 24.5 - - + +
534A LYS* 4.8 1.7 + - - -
----------------------------------------------------------
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