Contacts of the helix formed by residues 275 - 290 (chain A) in PDB entry 4R65
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 SER 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ARG* 3.5 26.9 - - - +
274A GLY* 1.3 76.6 + - - -
276A ASP* 1.3 67.2 + - - +
277A ILE 3.4 0.2 + - - -
278A PHE* 3.0 14.8 + - - +
279A ASN* 2.9 20.4 + - - -
333A ARG 3.0 14.4 + - - -
334A SER* 4.4 0.2 - - - -
335A GLU* 2.7 36.7 + - - -
401A DUP 3.9 2.7 - - - -
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Residues in contact with ASP 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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40A ARG* 2.6 38.8 + - - +
275A SER* 1.3 78.3 - - - +
277A ILE* 1.3 79.7 + - - +
279A ASN* 3.3 3.3 + - - +
280A LYS* 3.0 32.4 + - - +
335A GLU* 4.3 1.6 - - - +
401A DUP 3.5 57.5 + - + +
6T A 4.7 2.0 - - - +
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Residues in contact with ILE 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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40A ARG* 3.8 52.9 - - + +
41A LYS* 4.9 9.6 - - + +
44A SER* 3.8 17.0 - - - +
275A SER* 3.2 0.8 + - - -
276A ASP* 1.3 89.8 + - - +
278A PHE* 1.3 60.3 + - - +
280A LYS* 3.6 10.2 - - + +
281A ASN* 2.9 45.2 + - - +
335A GLU* 3.6 26.0 - - + +
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Residues in contact with PHE 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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270A LEU* 4.2 8.7 - - + -
274A GLY 3.7 13.2 - - - -
275A SER* 3.0 13.7 + - - +
277A ILE* 1.3 76.4 - - - +
279A ASN* 1.3 65.2 + - - +
281A ASN* 3.4 1.7 + - - +
282A MET* 2.8 51.2 + - - +
320A PHE* 3.7 27.1 - + - -
325A TRP* 3.8 9.9 - + - -
328A ARG* 3.5 44.2 - - - -
333A ARG* 3.2 46.7 - - + +
335A GLU* 3.7 16.9 - - - +
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Residues in contact with ASN 279 (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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270A LEU* 3.7 13.4 - - - +
271A TYR* 2.8 35.9 + - - +
274A GLY* 3.7 8.6 - - - -
275A SER 2.9 11.6 + - - +
276A ASP 3.5 7.6 - - - +
278A PHE* 1.3 85.5 - - - +
280A LYS* 1.3 60.0 + - - +
282A MET* 4.4 4.2 - - - +
283A ARG* 2.8 51.7 + - - +
401A DUP 3.0 30.3 + - - +
6T A 4.5 2.9 - - + -
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Residues in contact with LYS 280 (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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37A ASN* 2.9 43.8 + - - +
40A ARG* 4.6 13.9 - - - +
276A ASP 3.0 20.4 + - - +
277A ILE* 3.2 14.1 + - + +
279A ASN* 1.3 75.0 - - - +
281A ASN* 1.3 59.9 + - - +
284A ALA* 2.9 31.5 + - - +
6T A 3.2 82.0 + - + +
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Residues in contact with ASN 281 (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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41A LYS* 4.8 17.5 + - - +
44A SER* 5.4 1.2 + - - -
48A LYS* 5.2 4.6 - - - +
277A ILE* 2.9 30.8 + - - +
278A PHE* 3.6 4.3 - - + +
280A LYS* 1.3 77.4 - - - +
282A MET* 1.3 57.7 + - - +
284A ALA* 3.3 7.2 + - - +
285A HIS* 3.0 29.6 + - - +
325A TRP* 4.2 11.3 - - + -
335A GLU* 3.0 27.6 + - - +
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Residues in contact with MET 282 (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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270A LEU* 3.8 33.0 - - + -
278A PHE* 2.8 48.6 + - + +
279A ASN* 3.9 5.4 - - - +
281A ASN* 1.3 73.9 - - - +
283A ARG* 1.3 58.3 + - + +
285A HIS* 3.3 2.9 + - - +
286A ALA* 3.0 26.9 + - - +
293A ILE* 4.2 5.8 - - + -
319A ILE* 3.8 15.9 - - + -
320A PHE* 4.0 24.2 - - + +
323A ILE* 3.6 25.0 - - + +
325A TRP* 3.5 24.9 - - + -
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Residues in contact with ARG 283 (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 TYR* 3.4 34.2 - - - +
279A ASN* 2.8 31.8 + - - +
282A MET* 1.3 70.7 - - + +
284A ALA* 1.3 66.2 + - - +
286A ALA* 3.2 9.9 + - - +
287A LEU* 3.1 25.3 + - - +
293A ILE* 3.4 36.5 + - + +
294A ASN* 3.7 23.6 + - - +
295A GLU* 3.8 3.0 + - - +
6T A 3.0 64.0 + - - +
7T G 3.2 28.8 + - - +
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Residues in contact with ALA 284 (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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280A LYS 2.9 19.8 + - - +
281A ASN* 3.3 6.7 + - - +
283A ARG* 1.3 76.7 - - - +
285A HIS* 1.3 61.6 + - - +
287A LEU* 3.2 11.5 + - - +
288A GLU* 3.1 30.7 + - - +
5T C 5.4 2.5 - - - +
6T A 3.9 18.9 - - - +
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Residues in contact with HIS 285 (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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281A ASN 3.0 13.6 + - - +
282A MET 3.6 7.9 - - - +
283A ARG 3.2 0.2 - - - -
284A ALA* 1.3 72.2 - - - +
286A ALA* 1.3 66.1 + - - +
288A GLU* 3.0 24.3 + - + +
289A LYS* 2.8 46.4 + - + +
323A ILE* 2.9 38.1 + - + -
324A GLN 4.4 1.6 + - - -
325A TRP* 3.1 43.8 + + + -
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Residues in contact with ALA 286 (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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282A MET 3.0 12.9 + - - +
283A ARG* 3.3 10.8 - - - +
285A HIS* 1.3 76.0 - - - +
287A LEU* 1.3 52.0 + - - +
289A LYS* 2.9 4.8 + - - +
290A GLY 2.8 31.2 + - - -
291A PHE 2.8 20.6 + - - +
292A THR* 4.7 0.2 - - - -
293A ILE* 3.7 31.6 - - + +
323A ILE* 3.7 19.3 - - + +
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Residues in contact with LEU 287 (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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283A ARG 3.1 12.6 + - - +
284A ALA* 3.3 11.0 - - - +
286A ALA* 1.3 78.2 - - - +
288A GLU* 1.3 60.3 + - + +
290A GLY* 2.8 19.6 + - - -
291A PHE 3.2 15.7 + - - +
292A THR* 4.1 3.4 - - - -
301A LEU* 3.6 25.5 - - + +
5T C 4.4 18.2 - - - +
6T A 3.6 29.8 - - - +
7T G 3.5 24.0 - - - +
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Residues in contact with GLU 288 (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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284A ALA* 3.1 17.8 + - - +
285A HIS* 3.0 27.9 + - + +
287A LEU* 1.3 75.2 - - + +
289A LYS* 1.3 61.7 + - + +
290A GLY 3.5 0.3 + - - -
4D G 5.9 4.0 - - - +
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Residues in contact with LYS 289 (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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285A HIS* 2.8 41.5 + - + +
286A ALA 2.9 8.5 + - - +
288A GLU* 1.3 78.5 - - - +
290A GLY* 1.3 57.5 + - - +
291A PHE* 3.4 28.0 - - + -
322A TYR 5.6 0.2 - - - +
323A ILE* 3.6 24.2 - - - +
324A GLN* 2.9 41.4 + - - +
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Residues in contact with GLY 290 (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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286A ALA 2.8 5.1 + - - -
287A LEU 2.8 13.4 + - - -
288A GLU 3.2 1.2 + - - -
289A LYS* 1.3 79.4 - - - +
291A PHE* 1.3 60.5 + - - -
300A PRO* 3.6 6.2 - - - +
301A LEU* 3.0 35.3 + - - +
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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