Contacts of the helix formed by residues 270 - 282 (chain A) in PDB entry 2R4S
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 LYS 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A LEU* 3.5 18.8 - - - +
267A LYS* 2.7 11.7 + - + +
269A HIS* 1.3 84.8 - - + +
271A ALA* 1.3 53.1 + - - +
272A LEU 3.0 5.8 - - - -
273A LYS* 2.8 53.9 + - + +
274A THR* 2.9 9.9 + - - +
329A SER* 5.3 10.0 - - - +
55H SER* 3.3 20.0 - - - +
56H GLY* 5.2 1.5 - - - +
57H ASN* 3.0 33.5 + - - +
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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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141A TYR* 5.2 4.9 - - + +
267A LYS* 3.3 16.8 + - - +
268A GLU* 4.0 29.6 - - + +
269A HIS 3.5 0.4 - - - -
270A LYS* 1.3 78.7 - - - +
272A LEU* 1.3 58.3 + - + +
273A LYS 3.2 0.9 - - - -
274A THR* 2.7 28.1 - - + +
275A LEU* 3.3 18.0 - - + +
330A PRO* 6.1 0.4 - - - -
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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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131A ARG* 4.5 21.8 - - + -
135A ILE* 3.9 24.5 - - + -
141A TYR* 2.9 28.5 - - - +
219A TYR* 2.7 39.0 + - + +
222A VAL* 4.1 15.3 - - + -
223A PHE* 4.7 10.7 - - + -
226A ALA* 4.3 5.8 - - + -
264A PHE* 4.1 11.2 - - + -
268A GLU 3.6 13.7 + - - +
269A HIS* 4.1 9.6 - - - +
270A LYS 3.0 0.6 - - - -
271A ALA* 1.3 78.2 - - - +
273A LYS* 1.3 60.0 + - - +
274A THR 3.5 0.2 - - - -
275A LEU* 4.3 8.7 - - + +
276A GLY 3.0 8.8 + - - -
279A MET* 6.1 0.9 - - + -
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Residues in contact with LYS 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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223A PHE* 5.7 5.8 - - + -
269A HIS 3.9 4.6 + - - +
270A LYS* 2.9 50.8 - - + +
272A LEU* 1.3 78.7 - - - +
274A THR* 1.3 62.3 + - - +
275A LEU 3.3 0.2 - - - -
276A GLY* 3.1 9.4 + - - -
277A ILE* 3.1 33.4 + - + +
328A ARG 4.6 3.2 + - - -
329A SER* 3.0 28.3 + - - +
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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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72A ILE* 5.8 2.8 - - - +
270A LYS 2.9 8.0 + - - +
271A ALA* 2.7 42.2 - - + +
273A LYS* 1.3 77.8 - - - +
275A LEU* 1.3 67.0 + - + +
276A GLY 3.1 0.2 - - - -
277A ILE* 3.3 24.2 - - - +
278A ILE* 3.4 11.3 + - - +
325A ILE* 4.4 4.5 + - - +
326A TYR* 4.8 2.1 - - - +
329A SER* 4.1 19.9 - - - -
330A PRO* 3.6 33.9 - - + +
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Residues in contact with LEU 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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68A THR* 3.6 32.3 - - + -
72A ILE* 3.9 28.3 - - + -
127A ILE* 4.3 10.5 - - + -
131A ARG* 3.9 26.5 - - + -
141A TYR* 5.3 0.2 - - - +
271A ALA* 3.3 20.1 + - + +
272A LEU* 3.9 10.5 - - + -
273A LYS 3.3 0.2 - - - -
274A THR* 1.3 84.9 - - + +
276A GLY* 1.3 58.2 + - - +
278A ILE* 3.1 16.2 - - + +
279A MET* 2.8 46.7 - - + +
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Residues in contact with GLY 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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219A TYR* 2.8 35.2 + - - -
272A LEU 3.0 11.2 + - - -
273A LYS* 3.1 4.9 + - - -
274A THR 3.1 1.0 - - - -
275A LEU* 1.3 80.1 - - - +
277A ILE* 1.3 61.4 + - - +
280A GLY* 3.6 15.1 + - - -
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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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273A LYS* 3.4 24.9 - - + +
274A THR* 3.3 17.5 - - - +
276A GLY* 1.3 78.3 - - - +
278A ILE* 1.3 62.0 + - + +
279A MET 3.1 1.8 - - - -
280A GLY* 3.2 5.7 - - - +
281A THR* 2.7 37.7 + - - +
325A ILE* 3.4 32.5 - - + -
329A SER* 4.6 10.3 - - - +
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Residues in contact with ILE 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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72A ILE* 3.3 32.1 - - + -
75A LEU* 4.1 22.4 - - + -
124A LEU* 3.9 6.3 - - + +
274A THR 3.4 6.7 - - - +
275A LEU* 3.1 42.4 - - + +
277A ILE* 1.3 83.8 - - - +
279A MET* 1.3 63.4 + - + +
281A THR* 3.4 18.1 - - - +
282A PHE* 3.5 13.9 - - - +
322A ASN* 2.9 32.5 - - + +
325A ILE* 6.4 1.3 - - + -
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Residues in contact with MET 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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124A LEU* 3.2 43.5 - - + +
127A ILE* 4.7 14.1 - - + -
128A ALA* 4.2 17.3 - - - -
131A ARG* 5.8 2.2 - - + -
215A MET* 3.9 20.8 - - + +
219A TYR* 4.1 37.0 - - + -
272A LEU* 6.1 1.6 - - + -
275A LEU* 2.8 47.1 - - + +
276A GLY 4.5 2.5 - - - +
277A ILE 3.1 0.4 - - - -
278A ILE* 1.3 81.9 - - + +
280A GLY* 1.3 59.9 + - - +
281A THR 3.4 1.3 + - - -
282A PHE* 4.3 2.7 - - - +
283A THR* 3.8 17.5 + - - +
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Residues in contact with GLY 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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276A GLY 3.6 13.8 + - - -
277A ILE* 3.0 11.5 + - - -
279A MET* 1.3 80.6 - - - +
281A THR* 1.3 55.2 + - - +
283A THR* 3.3 20.8 - - - +
284A LEU* 4.1 10.7 - - - +
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Residues in contact with THR 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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277A ILE* 2.7 17.8 + - - +
278A ILE* 3.4 16.4 - - - +
280A GLY* 1.3 76.7 - - - +
282A PHE* 1.3 60.8 + - + +
283A THR 2.9 8.8 + - - -
284A LEU* 3.4 4.3 + - - +
285A CYS* 2.8 45.9 + - - +
318A ASN* 5.1 5.6 - - + +
321A PHE* 4.5 19.7 - - + +
322A ASN* 4.6 8.5 - - - +
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Residues in contact with PHE 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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75A LEU* 6.5 0.9 - - + -
117A VAL* 4.3 13.7 - - + -
120A SER* 3.1 27.4 - - - -
121A ILE* 3.4 43.3 - - + +
124A LEU* 4.3 18.2 - - + -
212A LEU* 5.9 0.5 - - - +
215A MET* 5.8 2.0 - - + -
278A ILE 3.5 16.8 + - - +
279A MET 4.3 2.4 - - - +
281A THR* 1.3 81.6 - - + +
283A THR* 1.3 58.9 + - - +
285A CYS* 4.1 4.9 - - - -
286A TRP* 3.4 52.2 + + + +
318A ASN* 4.1 15.5 - - + -
322A ASN* 6.0 2.5 - - - -
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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