Contacts of the helix formed by residues 266 - 278 (chain A) in PDB entry 2R5N
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLN* 2.9 21.7 + - - -
264A PRO* 3.2 3.0 - - - -
265A LEU* 1.3 78.5 - - - +
267A ASP* 1.3 60.5 + - - -
268A ALA 3.4 2.9 - - - -
269A GLU 3.2 3.6 + - - -
270A ILE* 2.9 29.5 + - - +
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Residues in contact with ASP 267 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLN* 3.4 29.6 + - - +
266A GLY* 1.3 71.9 - - - -
268A ALA* 1.3 63.2 + - - +
270A ILE* 3.2 8.6 + - - +
271A ALA* 3.0 22.9 + - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLY 3.4 0.8 - - - -
267A ASP* 1.3 76.3 - - - +
269A GLU* 1.3 64.2 + - - +
271A ALA* 3.2 9.6 + - - +
272A LEU* 3.2 28.5 + - + +
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Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A SER* 2.6 29.4 + - - +
252A PRO* 3.2 12.5 - - - +
253A ASN* 2.9 49.7 + - - +
254A LYS* 4.4 9.0 - - + -
265A LEU* 3.4 33.2 - - + +
266A GLY 3.2 2.8 + - - +
268A ALA* 1.3 80.3 - - - +
270A ILE* 1.3 57.8 + - - +
272A LEU* 3.2 7.6 + - - +
273A THR* 2.8 33.1 + - - +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 3.6 31.6 - - + +
17A ASP* 3.7 7.9 - - - +
20A GLN* 3.4 46.2 - - + +
265A LEU* 4.0 13.9 - - + -
266A GLY 2.9 14.7 + - - +
267A ASP* 3.2 8.0 + - - +
269A GLU* 1.3 77.1 - - - +
271A ALA* 1.3 57.1 + - - +
273A THR* 3.1 6.9 + - - -
274A ARG* 2.9 57.9 + - - +
283A PRO* 6.1 0.2 - - + -
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ASP 3.0 12.0 + - - +
268A ALA* 3.2 11.9 + - - +
270A ILE* 1.3 77.6 - - - +
272A LEU* 1.3 64.2 + - + +
274A ARG* 3.4 11.5 + - - +
275A GLU* 3.2 31.9 + - - +
676A EDO 5.5 0.2 - - - -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A PRO* 3.6 19.9 - - + +
253A ASN* 3.5 27.1 - - - +
268A ALA* 3.2 16.0 + - + +
269A GLU* 3.2 14.8 + - - +
271A ALA* 1.3 77.2 - - + +
273A THR* 1.3 57.2 + - - +
275A GLU* 3.3 20.5 + - - +
276A GLN* 2.9 28.6 + - - +
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 3.6 26.0 - - - -
31A MET* 3.7 13.0 - - + -
250A GLY 3.5 25.6 - - - +
251A SER* 3.3 21.7 - - - -
252A PRO* 4.2 0.2 - - - -
265A LEU* 4.2 3.6 - - - +
269A GLU 2.8 21.8 + - - -
270A ILE* 3.1 5.8 + - - -
272A LEU* 1.3 74.7 - - - +
274A ARG* 1.3 64.6 + - - +
276A GLN* 3.2 1.6 + - - +
277A LEU* 2.9 35.1 + - + +
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.5 0.8 - - - +
16A MET* 3.9 11.5 - - + +
17A ASP* 2.6 43.6 + - - -
270A ILE* 2.9 32.8 + - - +
271A ALA* 3.5 13.5 - - - +
273A THR* 1.3 74.0 - - - +
275A GLU* 1.3 57.7 + - - +
277A LEU* 4.8 0.2 - - - -
278A GLY* 2.9 25.5 + - - -
279A TRP* 3.0 46.0 + - + +
280A LYS 5.3 1.6 - - - -
281A TYR 2.8 31.2 + - - -
282A ALA* 3.4 3.2 + - - +
283A PRO* 3.3 22.7 - - - +
676A EDO 3.7 15.6 - - - -
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ALA* 3.2 19.0 + - - +
272A LEU* 3.6 27.2 - - - +
273A THR 3.2 0.8 - - - -
274A ARG* 1.3 77.6 - - - +
276A GLN* 1.3 63.3 + - - +
278A GLY* 3.4 10.2 + - - -
676A EDO 3.5 24.9 + - - +
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A PHE* 5.9 2.6 - - - -
250A GLY* 3.2 41.2 + - - +
251A SER 4.5 2.2 + - - -
252A PRO* 3.4 31.1 - - + +
272A LEU 2.9 13.6 + - - +
273A THR 3.8 0.2 - - - +
275A GLU* 1.3 77.6 - - - +
277A LEU* 1.3 62.7 + - + +
278A GLY 3.5 0.3 + - - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLU* 6.0 0.7 - - - +
9A ASN* 3.3 43.2 + - + +
12A ARG* 3.9 31.0 - - + -
13A ALA* 5.5 0.7 - - + +
16A MET* 4.8 6.1 - - + -
31A MET* 5.1 0.2 - - + -
249A PHE* 4.0 18.2 - - + -
250A GLY* 3.7 23.1 - - - -
273A THR* 2.9 37.4 + - + +
274A ARG 4.1 2.0 - - - +
276A GLN* 1.3 78.1 - - + +
278A GLY* 1.3 61.9 + - - +
279A TRP* 4.2 11.0 - - + +
677A EDO 5.2 1.0 + - - -
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ARG 2.9 7.5 + - - -
275A GLU 3.4 7.0 + - - -
276A GLN 3.3 4.6 + - - -
277A LEU* 1.3 78.1 - - - +
279A TRP* 1.3 52.0 + - - +
280A LYS* 3.6 0.7 + - - +
676A EDO 4.4 8.7 - - - -
677A EDO 2.6 32.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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