Contacts of the helix formed by residues 278 - 293 (chain B) in PDB entry 3O9Z
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 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.5 3.4 - - - -
123B ARG* 4.6 6.5 - - - -
124B VAL 3.3 16.4 - - - -
125B TYR* 4.0 8.3 - - - -
276B GLY 3.5 3.8 + - - -
277B PHE* 1.3 75.2 - - - +
279B LEU* 1.3 59.7 + - - -
280B ASP 3.3 2.7 - - - -
281B GLU* 2.8 19.1 + - - -
282B ALA* 2.9 27.7 + - - +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.9 14.8 - - + -
110B ILE* 3.8 28.9 - - + +
113B LEU* 3.7 30.3 - - + -
114B LYS* 3.6 41.1 - - + +
117B GLU* 3.4 36.6 - - - +
123B ARG* 5.1 3.6 - - - +
124B VAL* 3.9 13.5 + - + -
278B GLY* 1.3 70.7 - - - -
280B ASP* 1.3 64.9 + - - +
282B ALA* 3.3 1.1 + - - +
283B ALA* 3.0 28.4 + - - +
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 3.0 36.4 + - - +
278B GLY 3.3 0.6 - - - -
279B LEU* 1.3 80.5 - - - +
281B GLU* 1.3 72.5 + - - +
283B ALA* 3.9 11.0 + - - +
284B GLU* 4.9 1.9 + - - +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG* 5.5 2.1 + - - -
131B ARG* 3.0 44.6 + - - +
188B ASP* 3.8 1.4 - - - +
191B ALA* 5.9 1.4 - - - +
276B GLY 4.2 6.1 - - - +
277B PHE* 4.3 13.5 - - + -
278B GLY* 2.8 39.0 + - - +
280B ASP* 1.3 92.1 + - - +
282B ALA* 1.3 60.1 + - - +
283B ALA 3.6 0.3 + - - -
284B GLU* 4.5 5.5 + - - +
285B ALA 5.4 0.7 + - - -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.7 34.1 - - + -
110B ILE* 4.9 0.2 - - + -
126B THR* 4.2 12.1 - - + -
128B LEU* 4.7 4.3 - - + -
188B ASP* 4.4 7.8 - - - +
278B GLY 2.9 15.5 + - - +
279B LEU 4.1 1.6 - - - +
281B GLU* 1.3 77.1 - - - +
283B ALA* 1.3 66.2 + - - +
284B GLU 3.3 1.5 + - - -
285B ALA* 3.6 6.6 + - - +
286B ILE* 3.5 24.3 + - + +
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO* 5.7 0.5 - - - +
110B ILE* 3.9 29.7 - - + +
279B LEU 3.0 17.9 + - - +
280B ASP* 3.9 7.6 + - - +
281B GLU 3.4 2.4 - - - -
282B ALA* 1.3 77.0 - - - +
284B GLU* 1.3 65.1 + - - +
286B ILE* 3.2 5.0 + - - +
287B ARG* 3.0 22.8 + - - +
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Residues in contact with GLU 284 (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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191B ALA* 3.8 24.2 - - + -
195B GLY 4.2 1.8 - - - +
196B ARG* 3.7 28.2 + - + +
197B ALA 2.9 14.9 + - - -
216B LEU* 5.6 0.2 - - - +
280B ASP 4.9 2.7 + - - +
281B GLU 4.5 4.5 + - - +
282B ALA 3.4 0.8 - - - -
283B ALA* 1.3 77.7 - - - +
285B ALA* 1.3 64.3 + - - +
287B ARG* 2.8 47.9 + - - +
288B VAL* 3.0 31.2 + - + +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE* 3.6 14.6 - - + +
187B PHE* 3.6 12.7 - - + +
188B ASP* 3.4 49.9 + - + +
191B ALA* 4.6 2.5 - - + +
281B GLU 5.4 0.6 + - - -
282B ALA 3.6 4.9 + - - +
283B ALA 3.3 0.6 - - - -
284B GLU* 1.3 80.0 - - - +
286B ILE* 1.3 57.9 + - - +
288B VAL* 3.3 5.4 + - - +
289B ALA* 2.9 30.3 + - - +
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Residues in contact with ILE 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO* 4.7 2.2 - - + -
103B LEU* 4.0 13.2 - - + +
104B VAL 3.7 34.5 - - - +
105B LEU 3.9 11.6 - - - +
106B TRP 3.9 29.6 - - - +
107B PRO* 4.0 2.2 - - + -
110B ILE* 3.8 23.1 - - + -
184B ILE* 4.0 17.5 - - + -
282B ALA* 3.5 17.2 + - + +
283B ALA* 3.2 8.6 + - - +
285B ALA* 1.3 74.3 - - - +
287B ARG* 1.3 61.1 + - - +
289B ALA* 3.9 2.3 - - - +
290B ALA* 2.9 28.4 + - - +
293B ARG* 5.8 0.2 - - - +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO* 3.9 24.2 - - + +
196B ARG* 3.6 34.5 - - - +
197B ALA* 2.9 33.1 + - - +
283B ALA 3.0 12.6 + - - +
284B GLU* 2.8 48.4 + - - +
286B ILE* 1.3 77.8 - - - +
288B VAL* 1.3 63.6 + - - +
290B ALA* 3.8 1.6 - - - +
291B LEU* 3.1 52.2 + - + +
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 3.9 31.0 - - + +
197B ALA* 3.9 15.7 - - + -
200B VAL* 4.5 8.3 - - + -
214B LEU* 4.1 17.9 - - + -
216B LEU* 5.8 0.9 - - + -
284B GLU* 3.0 35.6 + - + +
285B ALA* 3.7 9.0 - - - +
287B ARG* 1.3 75.8 - - - +
289B ALA* 1.3 66.1 + - - +
291B LEU* 3.2 11.2 + - - +
292B LEU* 3.1 26.4 + - + +
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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
----------------------------------------------------------
179B ALA* 4.3 8.7 - - - +
180B THR* 3.4 30.3 + - + +
184B ILE* 4.1 15.9 - - + -
187B PHE* 4.8 4.2 - - + -
285B ALA 2.9 17.6 + - - +
286B ILE* 3.9 3.8 - - - +
288B VAL* 1.3 75.5 - - - +
290B ALA* 1.3 62.5 + - - +
292B LEU* 3.3 20.9 + - - +
293B ARG* 3.5 16.1 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU 4.0 2.0 - - - +
106B TRP* 4.0 12.3 - - + -
107B PRO* 3.7 23.8 - - + -
286B ILE 2.9 18.8 + - - +
287B ARG 3.8 2.9 - - - +
288B VAL 3.2 0.2 - - - -
289B ALA* 1.3 74.4 - - - +
291B LEU* 1.3 66.2 + - - +
293B ARG* 3.1 45.9 + - - +
294B THR* 4.3 4.3 + - - +
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Residues in contact with LEU 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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200B VAL* 4.4 26.0 - - + -
287B ARG* 3.1 46.6 + - + +
288B VAL* 3.2 10.5 + - - +
290B ALA* 1.3 75.5 - - - +
292B LEU* 1.3 65.2 + - + +
293B ARG 3.2 0.9 + - - -
294B THR* 3.3 8.4 + - - -
295B LEU* 3.1 27.9 + - + +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ALA* 4.2 16.6 - - + -
187B PHE* 3.4 41.7 - - + -
200B VAL* 3.8 25.6 - - + -
202B VAL* 3.9 28.9 - - + -
205B ARG* 2.8 29.5 + - - -
210B ASN* 5.9 1.3 - - - +
223B TRP* 4.1 13.2 - - + -
288B VAL* 3.1 21.1 + - + +
289B ALA* 3.5 10.1 - - - +
290B ALA 3.2 0.6 - - - -
291B LEU* 1.3 77.4 - - - +
293B ARG* 1.3 55.2 + - - +
294B THR 3.1 0.4 - - - -
295B LEU* 3.9 7.2 - - + -
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 2.9 38.9 + - - +
106B TRP* 3.3 47.0 - - + +
172B GLU* 3.8 31.0 - - - +
176B GLY* 2.9 33.1 + - - +
180B THR* 2.9 32.9 + - - +
205B ARG* 4.4 7.6 + - - +
286B ILE* 5.8 0.4 - - - +
289B ALA* 3.5 6.4 + - - +
290B ALA* 3.1 22.7 + - - +
292B LEU* 1.3 76.4 - - - +
294B THR* 1.3 67.9 + - + +
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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
------------------------------------------------------------
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