Contacts of the helix formed by residues 273 - 291 (chain B) in PDB entry 2WOE
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 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B GLY 4.4 5.4 + - - +
57B GLN* 6.4 1.3 - - - -
271B LYS 3.5 2.6 + - - -
272B LEU* 1.3 73.4 - - - +
274B MET* 1.3 61.0 + - - +
275B LYS* 3.0 24.9 + - - +
276B VAL* 3.2 23.1 + - + +
277B GLU* 2.9 24.8 + - - +
401C AR6 2.4 47.0 + - - -
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Residues in contact with MET 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B SER 5.9 1.8 - - - +
272B LEU 3.3 6.2 + - - +
273B ASP* 1.3 76.3 + - - +
275B LYS* 1.3 56.7 + - - +
277B GLU* 3.4 10.6 + - - +
278B ARG* 2.9 42.4 + - - +
208C GLN* 4.0 19.5 - - + +
209C SER 6.1 0.2 - - - +
210C SER* 3.9 18.4 - - - +
215C ASP* 3.8 22.4 - - - +
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Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASP* 3.0 13.6 + - - +
274B MET* 1.3 76.8 - - - +
276B VAL* 1.3 59.3 + - + +
278B ARG* 3.3 31.2 + - - +
279B GLU* 3.0 29.3 + - - +
121C GLU* 3.9 23.6 + - - -
122C GLY* 4.0 20.2 - - - -
401C AR6 3.3 46.0 + - + +
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.9 45.3 - - + -
66B LEU* 4.6 8.0 - - + +
272B LEU* 5.1 7.0 - - + -
273B ASP* 3.2 26.8 + - + +
275B LYS* 1.3 74.8 - - + +
277B GLU* 1.3 65.5 + - - +
279B GLU* 3.2 5.7 + - - +
280B ILE* 3.0 42.9 + - + +
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 3.9 19.7 - - + -
269B LEU* 3.5 29.5 - - - +
270B SER* 4.9 2.9 - - - -
272B LEU* 4.6 11.4 - - + +
273B ASP 2.9 15.4 + - - +
274B MET* 3.8 11.3 - - - +
276B VAL* 1.3 76.6 - - - +
278B ARG* 1.3 64.2 + - - +
280B ILE* 3.4 4.3 + - - +
281B ARG* 3.1 58.8 + - - +
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B MET* 2.9 24.6 + - - +
275B LYS* 3.3 44.1 + - - +
277B GLU* 1.3 75.7 - - - +
279B GLU* 1.3 58.4 + - - +
281B ARG* 3.3 11.2 + - - +
282B ARG* 3.0 27.7 + - - +
121C GLU* 5.1 3.6 + - - -
401C AR6 3.9 26.3 + - - -
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.9 22.2 - - + -
70B ARG* 4.1 15.9 + - - +
275B LYS 3.0 18.1 + - - +
276B VAL* 3.2 6.5 + - - +
278B ARG* 1.3 74.3 - - - +
280B ILE* 1.3 59.4 + - - +
282B ARG* 2.9 42.3 + - - +
283B GLN* 2.9 48.7 + - - +
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Residues in contact with ILE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 5.2 0.2 - - + -
14B PHE* 3.6 37.4 - - + +
15B LEU* 3.6 29.8 - - + +
18B ALA* 3.6 32.1 - - + -
62B THR* 4.5 4.5 - - + -
66B LEU* 4.0 22.0 - - + -
272B LEU* 4.7 1.1 - - + -
276B VAL* 3.0 30.8 + - + +
277B GLU* 3.6 6.3 - - - +
279B GLU* 1.3 74.5 - - - +
281B ARG* 1.3 59.3 + - - +
283B GLN* 3.3 3.1 + - - +
284B VAL* 2.9 31.7 + - + +
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Residues in contact with ARG 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B HIS* 5.4 0.2 + - - -
11B LEU* 3.6 41.4 - - + +
15B LEU* 3.7 22.1 - - + +
261B VAL* 4.9 4.6 - - - +
269B LEU* 4.8 8.3 - - - +
277B GLU* 3.1 48.8 + - - +
278B ARG* 3.6 12.1 - - - +
280B ILE* 1.3 77.0 - - - +
282B ARG* 1.3 62.0 + - - +
284B VAL* 3.4 2.6 + - - +
285B ASP* 3.1 29.3 + - - +
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 4.6 17.4 + - - +
73B ALA* 4.8 9.3 - - - +
278B ARG 3.0 14.2 + - - +
279B GLU* 2.9 45.1 + - - +
281B ARG* 1.3 75.5 - - - +
283B GLN* 1.3 71.3 + - - +
285B ASP* 3.3 8.2 + - - +
286B ALA* 2.9 38.9 + - + +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 3.8 15.2 - - + -
66B LEU* 3.0 46.9 + - - +
69B GLY* 3.3 22.4 - - - +
70B ARG* 3.5 17.9 - - - +
73B ALA* 5.5 1.3 - - + -
279B GLU* 2.9 43.3 + - - +
280B ILE 3.8 2.9 - - - +
282B ARG* 1.3 81.9 - - - +
284B VAL* 1.3 58.1 + - - +
286B ALA* 4.3 6.1 - - - -
287B LEU* 2.8 44.2 + - + +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B HIS* 4.1 13.9 - - + +
10B ALA* 3.9 22.2 - - + +
11B LEU* 3.9 21.8 - - + +
14B PHE* 3.8 32.1 - - + -
137B LEU* 4.7 4.7 - - + +
280B ILE* 2.9 22.0 + - + +
281B ARG 3.7 4.7 - - - +
283B GLN* 1.3 73.9 - - - +
285B ASP* 1.3 58.8 + - - +
287B LEU* 4.1 5.0 - - - +
288B LEU* 3.0 50.6 + - + +
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Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B HIS* 2.7 35.0 + - - -
281B ARG* 3.1 16.8 + - - +
282B ARG* 3.6 9.9 - - - +
284B VAL* 1.3 78.6 - - - +
286B ALA* 1.3 61.1 + - - +
288B LEU* 4.0 4.3 - - - +
289B ALA* 3.1 24.4 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA* 3.7 28.9 - - + +
282B ARG* 2.9 26.4 + - + +
283B GLN* 3.8 4.5 - - - +
285B ASP* 1.3 76.1 - - - +
287B LEU* 1.3 58.9 + - - +
289B ALA* 3.4 7.2 + - - +
290B LEU* 3.0 27.4 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 4.4 9.4 - - + -
69B GLY* 4.1 12.3 - - - +
72B LEU* 3.8 29.4 - - + -
73B ALA* 4.3 5.4 - - + +
134B PRO* 3.9 31.9 - - + +
137B LEU* 3.7 31.2 - - + +
138B ALA* 3.8 16.3 - - + +
283B GLN* 2.8 38.1 + - + +
284B VAL* 4.1 2.2 - - - +
286B ALA* 1.3 70.7 - - + +
288B LEU* 1.3 58.9 + - - +
290B LEU* 3.3 8.7 + - + +
291B ALA* 2.9 26.5 + - - +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.0 17.9 - - + -
7B HIS* 3.6 38.1 - - + +
10B ALA* 3.9 15.9 - - + -
137B LEU* 5.1 3.4 - - + +
140B LEU* 3.7 29.8 - - + -
284B VAL* 3.0 28.7 + - + +
285B ASP* 4.0 4.0 - - - +
287B LEU* 1.3 75.3 - - + +
289B ALA* 1.3 56.6 + - - +
291B ALA* 3.3 4.3 + - - +
292B GLY 2.9 6.9 + - - -
293B LEU* 2.7 55.3 + - + +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ASP 3.1 18.7 + - - +
286B ALA* 3.6 7.2 - - - +
287B LEU 3.3 0.2 - - - -
288B LEU* 1.3 75.6 - - - +
290B LEU* 1.3 62.3 + - - +
292B GLY* 3.1 14.4 + - - +
293B LEU 4.5 6.3 - - - +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 3.5 32.3 - - + +
73B ALA* 4.7 1.8 - - - +
76B GLY* 3.1 34.8 - - - +
77B THR* 4.2 1.6 - - - +
138B ALA* 4.0 25.8 - - + +
142B HIS* 3.5 16.0 + - - +
149B TRP* 4.8 7.0 - - + -
286B ALA 3.0 12.2 + - - +
287B LEU* 3.4 13.5 - - + +
289B ALA* 1.3 78.4 - - - +
291B ALA* 1.3 58.7 + - - +
292B GLY 3.6 0.2 + - - -
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU 3.5 24.5 - - - +
138B ALA 3.8 6.9 + - - -
140B LEU* 3.9 9.0 - - + +
141B GLY* 3.2 41.4 - - - +
142B HIS* 4.2 4.5 - - - -
287B LEU 2.9 8.2 + - - +
288B LEU* 3.3 11.6 + - - +
290B LEU* 1.3 77.2 - - - +
292B GLY* 1.3 58.6 + - - +
293B LEU* 4.3 7.2 - - + +
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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
------------------------------------------------------------
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