Contacts of the helix formed by residues 269 - 284 (chain A) in PDB entry 5W97
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 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A PRO 3.5 1.6 + - - -
268A PHE* 1.3 85.9 - - - +
270A TYR* 1.3 67.6 + - - +
271A MET 3.2 3.1 - - - -
272A GLY* 2.9 6.1 + - - -
273A MET* 2.9 23.8 + - - +
56B MET 5.4 2.2 + - - -
58B ALA* 4.0 12.8 - - - +
62B GLU* 3.9 12.9 - - - +
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Residues in contact with TYR 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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178A GLN 3.4 0.2 + - - -
179A TYR* 3.2 32.9 - - - -
181A THR 2.7 29.4 + - - -
182A PRO* 4.8 1.6 - - + -
183A LEU* 3.6 30.3 - - + -
186A TRP* 3.0 20.8 + - - -
266A GLU* 4.8 4.0 - - + +
267A PRO* 4.0 18.9 + - + +
268A PHE 3.4 2.4 - - - -
269A GLY* 1.3 73.9 - - - +
271A MET* 1.3 87.1 + - + +
273A MET* 3.1 12.7 + - - +
274A VAL* 3.1 26.3 + - + +
67F SER* 3.3 32.5 - - - +
68F THR* 5.9 1.1 - - - -
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Residues in contact with MET 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR* 3.7 34.8 - - + -
269A GLY 3.2 1.2 - - - -
270A TYR* 1.3 104.0 - - + +
272A GLY* 1.3 57.4 + - - +
274A VAL* 3.3 7.1 + - + +
275A TRP* 2.8 29.3 + - - +
59B GLN* 5.5 4.9 - - - +
303B CHD 3.6 60.3 - - + +
67F SER* 5.7 0.9 - - - -
14g ARG* 3.8 15.0 - - + +
18g PHE* 4.3 17.6 - - + -
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Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLY* 2.9 9.4 + - - -
271A MET* 1.3 73.1 - - - +
273A MET* 1.3 60.4 + - - +
275A TRP* 3.7 5.1 - - - +
276A ALA* 2.7 35.7 + - - +
318A VAL* 3.9 3.2 - - - +
62B GLU* 4.3 18.4 - - - -
303B CHD 4.0 18.8 - - - +
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Residues in contact with MET 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.7 26.0 - - + -
255A SER* 4.6 9.9 - - - -
267A PRO* 5.2 2.9 - - + -
268A PHE 3.8 9.2 - - - +
269A GLY 2.9 17.7 + - - +
270A TYR 3.1 7.4 + - - +
272A GLY* 1.3 77.4 - - - +
274A VAL* 1.3 64.4 + - - +
276A ALA* 3.4 0.7 + - - -
277A MET* 3.1 23.7 + - - +
318A VAL* 3.7 5.2 - - + +
319A LYS* 3.3 56.7 + - + +
322A SER* 3.2 37.2 - - - +
323A TRP* 4.7 4.7 - - - -
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR* 5.0 2.5 - - + -
183A LEU* 3.9 9.0 - - + -
186A TRP* 3.7 48.9 - - + +
190A ILE* 4.6 0.3 - - - +
270A TYR* 3.1 25.7 + - + +
271A MET* 3.5 10.5 - - - +
273A MET* 1.3 72.9 - - - +
275A TRP* 1.3 65.7 + - - +
277A MET* 3.4 9.5 + - - +
278A MET* 3.1 46.8 + - + +
18g PHE* 4.1 11.9 - - + -
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Residues in contact with TRP 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A MET 2.8 20.1 + - - +
272A GLY 3.7 7.4 - - - +
274A VAL* 1.3 73.4 - - - +
276A ALA* 1.3 68.3 + - + +
278A MET* 3.4 4.4 + - + +
279A SER* 2.7 50.5 + - - -
314A ILE* 4.5 8.1 - - + -
315A PRO* 3.9 23.3 - - + -
318A VAL* 3.9 20.9 - - + -
66B THR* 5.0 0.7 - - - -
303B CHD 3.8 56.3 - - + -
303c PEK 3.7 32.8 - - + -
18g PHE* 3.8 21.7 - + + -
22g GLY* 2.8 41.2 + - - -
26g PRO* 5.8 0.2 - - + -
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Residues in contact with ALA 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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272A GLY 2.7 21.2 + - - +
273A MET* 3.6 3.4 - - - +
274A VAL 3.2 0.2 - - - -
275A TRP* 1.3 83.6 - - + +
277A MET* 1.3 56.5 + - - +
279A SER* 3.7 1.2 - - - -
280A ILE* 2.9 37.6 + - - +
315A PRO* 3.4 29.2 - - + +
318A VAL* 4.4 3.8 - - + -
319A LYS* 3.6 20.6 - - + -
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Residues in contact with MET 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.9 19.7 - - + +
186A TRP* 3.9 28.7 - - + -
187A SER* 3.7 25.6 - - - +
190A ILE* 3.5 21.2 - - + +
248A LEU* 4.0 20.6 - - + +
251A PHE* 4.6 5.4 - - - -
252A GLY* 5.0 2.0 - - - -
273A MET 3.1 24.6 + - - +
274A VAL* 3.9 3.6 - - - +
276A ALA* 1.3 73.7 - - - +
278A MET* 1.3 57.9 + - - +
280A ILE* 3.5 7.2 + - - +
281A GLY* 3.0 25.5 + - - -
319A LYS* 3.7 28.3 - - + +
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Residues in contact with MET 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR* 5.3 1.1 - - + +
186A TRP* 3.4 37.0 - - + -
190A ILE* 4.0 13.2 - - + -
274A VAL* 3.1 27.9 + - + +
275A TRP* 3.7 5.8 - - + +
277A MET* 1.3 73.2 - - - +
279A SER* 1.3 59.4 + - - +
281A GLY* 3.2 2.9 + - - -
282A PHE* 2.9 28.7 + - - +
4g ALA 3.7 5.5 - - - +
5g LYS* 3.4 42.0 - - + +
6g GLY 3.6 13.0 - - - +
7g ASP* 5.5 0.9 - - + -
18g PHE* 3.9 23.3 - - + -
19g LEU* 5.6 5.2 - - - -
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TRP* 2.7 46.6 + - - -
276A ALA 3.7 3.4 - - - -
278A MET* 1.3 74.2 - - - +
280A ILE* 1.3 59.3 + - - +
282A PHE* 3.0 7.4 + - - +
283A LEU* 2.8 36.8 + - - +
315A PRO* 3.9 17.9 - - - -
303c PEK 4.1 19.9 - - - +
22g GLY 4.8 0.3 + - - -
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Residues in contact with ILE 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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244A TYR* 3.7 37.2 - - + +
248A LEU* 4.5 11.4 - - + -
251A PHE* 4.0 24.2 - - + -
276A ALA 2.9 25.9 + - - +
277A MET* 3.7 6.3 - - - +
279A SER* 1.3 75.7 - - - +
281A GLY* 1.3 57.0 + - - +
283A LEU* 4.0 4.0 - - - +
284A GLY* 3.0 27.0 + - - -
312A ILE* 4.2 8.7 - - + +
315A PRO* 3.9 17.7 - - + -
316A THR* 3.8 30.7 - - - +
319A LYS* 4.5 5.8 - - + -
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Residues in contact with GLY 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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190A ILE* 4.5 3.8 - - - -
194A LEU* 3.6 28.6 - - - +
248A LEU* 5.2 0.9 - - - -
277A MET 3.0 15.2 + - - -
278A MET 3.2 4.5 + - - -
280A ILE* 1.3 78.5 - - - +
282A PHE* 1.3 61.0 + - - +
284A GLY* 3.6 4.3 + - - -
285A PHE* 3.4 22.5 + - - -
4g ALA 3.8 9.6 - - - -
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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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278A MET 2.9 10.5 + - - +
279A SER* 3.0 8.9 + - - +
281A GLY* 1.3 75.2 - - - +
283A LEU* 1.3 73.3 + - + +
284A GLY 3.2 0.5 + - - -
285A PHE* 3.3 17.4 + - + +
286A ILE* 4.3 16.0 + - + +
303c PEK 4.8 5.8 - - + -
1g ALA* 6.1 0.9 - - + -
2g SER 5.8 0.7 - - - -
3g ALA* 3.8 33.0 - - - -
4g ALA 3.8 1.3 + - - -
5g LYS* 3.3 32.1 - - - +
23g LEU* 4.8 8.7 - - + -
103g CDL 3.7 76.5 - - + -
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Residues in contact with LEU 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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279A SER* 2.8 22.1 + - - +
280A ILE 4.9 0.2 - - - +
282A PHE* 1.3 77.0 - - + +
284A GLY* 1.3 58.8 + - - +
285A PHE 3.0 5.4 + - - -
286A ILE* 3.1 34.5 + - + +
287A VAL* 3.3 17.8 - - + +
308A ALA* 4.7 4.3 - - - +
311A ILE* 3.8 37.7 - - + -
312A ILE* 3.4 34.3 - - + -
315A PRO* 4.2 13.7 - - + -
303c PEK 4.4 10.8 - - + -
103g CDL 4.4 21.8 - - + -
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Residues in contact with GLY 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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194A LEU* 6.1 1.6 - - - -
240A HIS* 3.1 39.2 - - - +
241A PRO* 3.4 16.6 - - - +
244A TYR* 4.3 4.9 - - - -
280A ILE 3.0 18.3 + - - -
281A GLY 4.1 3.6 - - - -
282A PHE 3.1 1.2 - - - -
283A LEU* 1.3 76.7 - - - +
285A PHE* 1.4 60.3 + - - +
286A ILE 3.5 0.2 - - - -
287A VAL* 4.0 3.9 + - - +
288A TRP* 5.5 0.3 + - - +
312A ILE* 3.9 3.3 - - - +
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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
------------------------------------------------------------
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