Contacts of the helix formed by residues 263 - 278 (chain A) in PDB entry 4RA2
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 ASP 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLN* 4.3 6.8 - - - +
23A ARG* 5.0 1.3 - - - +
261A THR* 3.2 15.1 + - - +
262A ASP* 1.3 79.8 + - - +
264A LEU* 1.3 63.1 + - - +
265A GLU* 3.2 12.5 + - - +
266A LYS* 3.1 32.3 + - + +
267A VAL* 3.1 23.1 + - - +
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Residues in contact with LEU 264 (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 GLN* 5.1 3.9 + - + -
18A GLN* 6.2 0.2 - - - +
23A ARG* 3.5 53.2 - - + +
24A TYR* 3.6 15.5 - - - +
25A GLY* 3.6 17.5 - - - +
258A LEU* 3.7 30.3 - - + -
262A ASP* 3.2 14.9 + - - +
263A ASP* 1.3 70.7 + - - +
265A GLU* 1.3 65.9 + - - +
267A VAL* 3.3 4.3 + - - +
268A CYS* 3.0 27.7 + - - -
288A LEU* 4.1 10.3 - - + +
290A CYS* 3.9 19.1 - - - -
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Residues in contact with GLU 265 (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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14A ASN* 3.5 32.7 + - + +
15A ALA* 3.0 45.0 + - - +
16A GLN* 3.3 32.1 + - + +
25A GLY* 4.5 0.7 - - - -
26A LEU 4.3 4.7 - - - +
263A ASP* 3.2 7.8 + - - +
264A LEU* 1.3 77.5 - - - +
266A LYS* 1.3 58.1 + - - +
268A CYS* 3.3 3.4 + - - +
269A ASN* 2.9 36.1 + - - +
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Residues in contact with LYS 266 (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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260A VAL* 5.6 6.2 - - - +
261A THR* 4.3 24.6 + - + +
263A ASP* 3.1 32.0 + - + +
265A GLU* 1.3 78.9 - - - +
267A VAL* 1.3 57.6 + - - +
269A ASN* 3.2 11.1 + - + +
270A GLU* 2.9 59.2 + - + +
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Residues in contact with VAL 267 (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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254A VAL* 4.3 18.8 - - + -
257A ARG* 3.9 24.7 - - + +
258A LEU* 4.0 20.0 - - + -
261A THR* 3.5 23.6 - - + +
263A ASP 3.1 15.4 + - - +
264A LEU* 3.7 6.1 - - - +
265A GLU 3.3 0.2 - - - -
266A LYS* 1.3 75.0 - - - +
268A CYS* 1.3 63.1 + - - +
270A GLU* 3.2 10.4 + - - +
271A VAL* 3.0 24.4 + - + +
288A LEU* 3.7 23.3 - - + -
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Residues in contact with CYS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 3.4 26.7 - - - -
26A LEU* 3.7 2.7 - - - -
27A SER* 3.6 15.9 - - - +
264A LEU 3.0 20.7 + - - +
265A GLU 3.7 2.9 - - - +
267A VAL* 1.3 78.1 - - - +
269A ASN* 1.3 55.6 + - - +
271A VAL* 3.2 7.1 + - - +
272A VAL* 3.0 32.4 + - - +
286A VAL* 3.3 29.7 - - + +
288A LEU* 3.6 21.8 - - - -
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Residues in contact with ASN 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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12A LYS* 3.5 25.2 - - - +
14A ASN* 2.9 30.4 - - - +
27A SER* 2.8 28.3 + - - -
265A GLU* 2.9 20.2 + - - +
266A LYS* 3.5 11.2 - - + +
268A CYS* 1.3 75.2 - - - +
270A GLU* 1.3 59.1 + - + +
272A VAL* 3.8 1.0 - - - +
273A ASP* 2.9 37.0 + - - +
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Residues in contact with GLU 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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253A PHE* 4.3 13.5 - - + -
257A ARG* 3.5 38.7 + - + +
260A VAL* 6.0 1.6 - - - +
261A THR* 4.7 2.8 - - - +
266A LYS* 2.9 44.4 + - + +
267A VAL* 3.2 16.2 + - - +
269A ASN* 1.3 77.4 - - + +
271A VAL* 1.3 56.5 + - - +
273A ASP* 4.2 4.1 - - - +
274A THR* 2.8 36.2 + - - +
305A GLU* 5.5 0.5 - - - +
353A SER 6.2 0.4 - - - +
356A ASN* 5.9 3.8 - - - +
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Residues in contact with VAL 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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241A ILE* 4.1 24.2 - - + -
245A MET* 5.3 0.4 - - - -
250A LEU* 3.8 23.8 - - + -
253A PHE* 4.2 15.0 - - + -
254A VAL* 4.0 26.7 - - + -
267A VAL* 3.0 22.3 + - + +
268A CYS* 3.2 10.5 + - - +
270A GLU* 1.3 77.3 - - - +
272A VAL* 1.3 63.9 + - - +
274A THR* 3.3 2.3 + - - -
275A CYS* 3.0 26.2 + - - -
286A VAL* 4.6 17.0 - - + -
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Residues in contact with VAL 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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12A LYS* 3.9 4.9 - - + -
27A SER* 3.9 22.2 - - - +
29A MET* 3.4 45.1 - - + -
241A ILE* 4.2 11.7 - - + -
268A CYS 3.0 20.1 + - - +
269A ASN 3.8 3.4 - - - +
271A VAL* 1.3 75.9 - - - +
273A ASP* 1.3 57.1 + - - +
275A CYS 3.3 0.9 + - - -
276A LEU* 3.0 25.6 + - - +
284A MET* 3.6 27.1 - - + +
286A VAL* 4.2 15.0 - - + -
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Residues in contact with ASP 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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10A MET* 5.0 5.4 - - - +
12A LYS* 2.7 35.3 + - - -
29A MET* 4.1 6.8 - - - +
269A ASN* 2.9 19.8 + - - +
270A GLU* 4.2 3.1 - - - +
272A VAL* 1.3 73.0 - - - +
274A THR* 1.3 67.2 + - - +
276A LEU* 3.2 6.7 + - - +
277A TYR* 2.9 47.0 + - + -
356A ASN* 2.8 32.4 + - - +
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Residues in contact with THR 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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245A MET* 4.2 8.1 - - - -
253A PHE* 3.7 8.0 - - + -
270A GLU* 2.8 23.3 + - - +
271A VAL 3.6 4.3 - - - -
273A ASP* 1.3 78.0 - - - +
275A CYS* 1.3 57.5 + - - +
277A TYR* 3.2 4.1 + - - +
278A LYS* 2.9 54.3 + - + +
349A GLY* 3.9 18.2 - - - +
352A ALA* 3.9 8.2 - - + +
353A SER* 3.2 30.0 + - - +
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Residues in contact with CYS 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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240A GLY 4.2 1.3 - - - +
241A ILE* 3.6 28.5 - - + -
244A VAL* 3.6 24.5 - - + +
245A MET* 3.6 27.1 - - - -
271A VAL* 3.0 21.7 + - - +
274A THR* 1.3 72.5 - - - +
276A LEU* 1.3 66.9 + - - +
278A LYS* 3.3 9.6 + - - +
279A GLY 3.3 0.9 + - - -
280A SER* 2.9 24.4 + - - -
284A MET* 3.7 18.4 - - - -
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Residues in contact with LEU 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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8A PRO* 4.3 10.8 - - + -
10A MET* 4.3 15.9 - - + -
29A MET* 4.1 15.3 - - + -
31A GLY* 4.8 2.2 - - - -
32A TRP* 3.6 28.9 + - + +
272A VAL 3.0 13.7 + - - +
273A ASP* 3.5 10.3 - - - +
275A CYS* 1.3 76.4 - - - +
277A TYR* 1.3 82.9 - - + +
279A GLY* 2.9 21.0 + - - -
280A SER 3.6 19.9 + - - +
284A MET* 3.8 18.0 - - + +
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Residues in contact with TYR 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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10A MET* 4.4 17.5 - - + +
273A ASP* 2.9 38.8 + - + +
274A THR 3.7 3.8 - - - +
276A LEU* 1.3 99.0 - - + +
278A LYS* 1.3 58.6 + - - +
279A GLY* 3.1 2.2 + - - -
352A ALA* 3.4 35.0 - - + +
355A ARG* 3.4 52.9 + - + +
356A ASN* 2.7 35.7 + - - -
359A GLU* 4.5 2.6 + - - -
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Residues in contact with LYS 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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244A VAL* 3.8 24.6 + - + +
245A MET* 3.6 28.9 - - + +
249A GLU* 5.0 4.8 + - - -
274A THR* 2.9 38.9 + - + +
275A CYS* 3.7 6.7 - - - +
276A LEU 3.2 0.4 - - - -
277A TYR* 1.3 76.2 - - - +
279A GLY* 1.3 57.3 + - - +
280A SER 3.7 0.7 - - - -
348A GLY 2.9 28.3 + - - -
349A GLY 3.6 9.8 + - - -
350A GLU* 4.5 6.7 - - - +
352A ALA* 3.7 10.7 - - + +
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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