Contacts of the helix formed by residues 280 - 292 (chain A) in PDB entry 4G17
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 PHE 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 4.3 27.1 - - + -
240A MET* 4.0 18.2 - - + -
243A LEU* 4.1 50.5 - - + -
244A ARG* 5.3 3.8 - - + -
277A CYS* 2.9 15.1 + - - +
278A GLU 3.5 15.9 - - - -
279A ASN* 1.3 90.2 - - + +
281A PRO* 1.3 57.7 - - - +
282A GLU* 3.2 3.1 - - - -
283A MET* 2.9 38.5 + - + +
284A ALA 3.2 8.1 + - - -
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Residues in contact with PRO 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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274A GLU* 5.7 2.2 - - - +
277A CYS 5.1 0.4 - - - +
279A ASN* 3.5 8.3 - - - +
280A PHE* 1.3 87.6 - - - +
282A GLU* 1.3 77.7 + - - +
284A ALA* 3.1 11.2 + - + +
285A THR* 3.0 25.2 + - - -
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Residues in contact with GLU 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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280A PHE* 3.2 1.3 - - - -
281A PRO* 1.3 88.4 - - - +
283A MET* 1.3 61.2 + - + +
285A THR* 3.2 7.3 + - - -
286A TYR* 2.9 29.8 + - - +
307A LEU* 3.7 31.5 - - + +
308A PHE* 4.1 15.2 - - + -
311A LEU* 3.6 34.4 - - + +
314A ARG* 3.0 27.8 + - - -
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Residues in contact with MET 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 5.2 2.2 - - + -
139A VAL* 4.2 10.1 - - + -
140A LEU* 4.3 13.5 - - + -
143A ALA* 5.1 1.6 - - + -
236A GLY* 5.4 1.1 - - - +
239A PHE* 3.9 31.2 - - + -
240A MET* 3.4 31.6 - - + +
243A LEU* 3.9 22.4 - - + -
277A CYS* 4.0 3.8 - - - -
280A PHE* 2.9 20.5 + - + +
282A GLU* 1.3 78.8 - - + +
284A ALA* 1.3 57.7 + - - +
286A TYR* 3.4 6.5 + - - +
287A LEU* 3.0 30.1 + - - +
308A PHE* 3.7 33.7 - - + -
311A LEU* 6.1 0.7 - - + -
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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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273A ILE* 3.6 18.9 - - + +
274A GLU* 4.3 8.7 - - - +
277A CYS* 3.9 13.4 - - + +
280A PHE 3.2 2.9 + - - +
281A PRO* 3.1 14.3 + - + +
283A MET* 1.3 77.7 - - - +
285A THR* 1.3 60.3 + - - +
287A LEU 3.5 0.2 + - - -
288A ARG* 2.9 60.0 + - - +
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Residues in contact with THR 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 PRO 3.0 14.0 + - - -
282A GLU* 3.2 9.4 + - - -
284A ALA* 1.3 76.3 - - - +
286A TYR* 1.3 63.5 + - - +
288A ARG* 3.9 8.9 + - - +
289A TYR* 3.1 22.7 + - + +
303A TYR* 3.4 25.4 - - - +
307A LEU* 3.8 18.4 - - + -
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Residues in contact with TYR 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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147A ILE* 4.0 19.2 - - + +
232A LEU* 2.9 43.1 + - - +
235A LEU* 3.8 10.7 - - - +
236A GLY* 3.7 20.4 - - - -
239A PHE* 4.1 8.5 - + - -
282A GLU 2.9 17.8 + - - +
283A MET* 3.6 7.0 - - - +
285A THR* 1.3 76.5 - - - +
287A LEU* 1.3 69.1 + - + +
289A TYR* 3.1 7.2 + - - +
290A VAL* 3.0 38.0 + - + +
304A LEU* 3.6 33.7 - - + -
307A LEU* 3.9 12.3 - - + +
308A PHE* 3.7 28.9 - + + -
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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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233A GLU* 4.0 28.7 - - + +
236A GLY* 4.0 15.7 - - - -
237A HIS* 4.3 9.0 - - + -
240A MET* 4.9 6.1 - - + -
273A ILE* 4.1 11.7 - - + -
276A LEU* 3.9 27.8 - - + -
277A CYS* 4.1 13.9 - - - -
283A MET 3.0 13.2 + - - +
284A ALA 3.9 2.9 - - - +
286A TYR* 1.3 79.2 - - + +
288A ARG* 1.3 58.5 + - - +
290A VAL* 3.2 11.5 - - + +
291A ARG* 3.0 55.9 + - + +
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Residues in contact with ARG 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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273A ILE* 3.4 34.5 - - + +
274A GLU* 2.7 50.3 + - - +
284A ALA* 2.9 32.9 + - - +
285A THR* 3.9 7.6 + - - +
287A LEU* 1.3 76.7 - - - +
289A TYR* 1.3 62.5 + - - +
291A ARG* 4.1 1.9 - - - +
292A ARG* 3.1 61.3 + - - +
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Residues in contact with TYR 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 THR 3.1 14.0 + - - +
286A TYR 3.4 7.9 - - - +
288A ARG* 1.3 74.8 - - - +
290A VAL* 1.3 72.9 + - + +
292A ARG* 3.2 14.7 + - - +
293A LEU* 3.2 45.5 + - + +
297A GLU* 5.2 2.2 + - - -
298A LYS 4.7 0.7 + - - -
299A PRO* 3.8 1.0 - - + +
300A ASP* 2.9 38.0 + - + +
303A TYR* 3.8 27.8 - + + +
304A LEU* 3.5 31.4 - - + -
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Residues in contact with VAL 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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229A ARG* 4.1 10.7 - - - +
232A LEU* 3.8 22.7 - - + -
233A GLU* 3.8 33.5 - - + +
286A TYR* 3.0 22.7 + - + +
287A LEU* 3.2 22.7 - - + +
289A TYR* 1.3 86.7 - - + +
291A ARG* 1.3 65.6 + - - +
293A LEU* 3.1 31.5 + - + +
304A LEU* 3.9 13.9 - - + -
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 3.6 30.0 - - - +
219A ASN* 4.7 12.1 + - - -
229A ARG* 5.5 0.7 + - - -
233A GLU* 3.2 39.6 + - + +
237A HIS* 3.0 29.9 + - - -
249A TRP* 4.9 4.0 - - - -
268A LYS* 4.6 11.3 + - - +
271A THR 4.9 4.9 + - - -
273A ILE* 3.6 30.9 - - + +
276A LEU* 4.6 7.7 - - - +
287A LEU* 3.0 36.6 + - + +
288A ARG* 4.1 5.4 - - - +
290A VAL* 1.3 77.6 - - - +
292A ARG* 1.3 62.0 + - + +
293A LEU 3.8 3.2 + - - +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ARG* 3.1 49.2 + - - +
289A TYR* 3.2 7.7 + - - +
290A VAL 3.1 0.8 - - - -
291A ARG* 1.3 81.6 - - + +
293A LEU* 1.3 65.8 + - - +
294A ASP 3.6 0.9 + - - -
297A GLU* 4.6 1.2 - - - +
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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