Contacts of the helix formed by residues 279 - 293 (chain A) 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 LEU 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.9 16.6 - - + -
110A ILE* 3.8 28.8 - - + +
113A LEU* 3.7 26.9 - - + -
114A LYS* 3.4 47.1 - - + +
117A GLU* 3.4 34.3 - - + +
123A ARG* 5.0 3.6 - - - +
124A VAL* 3.8 10.0 + - + -
278A GLY* 1.3 71.0 - - - -
280A ASP* 1.3 63.4 + - - +
282A ALA* 3.9 0.3 - - - +
283A ALA* 3.0 28.6 + - - +
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Residues in contact with ASP 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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114A LYS* 3.0 33.7 + - - +
123A ARG* 6.0 0.4 - - - +
278A GLY 3.2 0.4 - - - -
279A LEU* 1.3 80.6 - - - +
281A GLU* 1.3 70.8 + - - +
283A ALA* 3.9 10.7 + - - +
284A GLU* 4.9 1.9 + - - +
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Residues in contact with GLU 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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123A ARG* 5.3 2.1 + - - -
131A ARG* 3.1 43.5 + - - +
188A ASP* 3.9 1.6 - - - +
191A ALA* 5.9 1.2 - - - +
276A GLY 4.3 6.8 - - - +
277A PHE* 4.2 14.1 - - + -
278A GLY* 2.9 37.8 + - - +
280A ASP* 1.3 85.8 + - - +
282A ALA* 1.3 62.7 + - - +
283A ALA 3.5 0.3 + - - -
284A GLU* 4.4 6.4 + - - +
285A ALA 5.3 0.5 + - - -
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Residues in contact with ALA 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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103A LEU* 3.6 30.5 - - + +
110A ILE* 4.9 0.7 - - + -
126A THR* 4.1 15.0 - - + -
128A LEU* 4.6 4.5 - - + -
188A ASP* 4.3 9.0 - - - -
278A GLY 2.9 16.2 + - - +
279A LEU 3.3 2.0 + - - +
281A GLU* 1.3 77.4 - - - +
283A ALA* 1.3 67.0 + - - +
284A GLU 3.3 1.0 + - - -
285A ALA* 3.5 7.0 + - - +
286A ILE* 3.3 26.3 + - + +
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Residues in contact with ALA 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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107A PRO* 5.7 0.3 - - - +
110A ILE* 4.1 28.0 - - + +
279A LEU 3.0 17.9 + - - +
280A ASP* 4.2 8.3 - - - +
281A GLU 3.3 1.8 - - - -
282A ALA* 1.3 78.9 - - - +
284A GLU* 1.3 64.5 + - - +
286A ILE* 3.2 4.9 + - - +
287A ARG* 3.0 22.8 + - - +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ALA* 3.7 25.8 - - + -
195A GLY 4.3 1.1 - - - +
196A ARG* 3.6 29.2 + - + +
197A ALA 2.9 15.6 + - - -
280A ASP 4.9 2.3 + - - +
281A GLU 4.4 5.4 + - - +
282A ALA 3.3 1.0 + - - -
283A ALA* 1.3 77.7 - - - +
285A ALA* 1.3 64.6 + - - +
287A ARG* 2.8 46.2 + - - +
288A VAL* 3.0 33.1 + - + +
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Residues in contact with ALA 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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184A ILE* 3.6 15.7 - - + +
187A PHE* 3.7 12.8 - - + +
188A ASP* 3.4 50.0 + - + +
191A ALA* 4.5 1.6 - - + +
281A GLU 5.3 0.4 + - - -
282A ALA 3.5 4.5 + - - +
283A ALA 3.3 0.4 - - - -
284A GLU* 1.3 80.3 - - - +
286A ILE* 1.3 57.1 + - - +
288A VAL* 3.4 5.0 + - - +
289A ALA* 2.9 30.8 + - - +
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Residues in contact with ILE 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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102A PRO* 4.7 2.5 - - + -
103A LEU* 3.9 13.9 - - + +
104A VAL 3.6 39.0 - - - +
105A LEU 4.0 7.0 - - - +
106A TRP 3.9 28.3 - - - +
107A PRO* 4.0 2.7 - - + -
110A ILE* 3.9 23.1 - - + -
184A ILE* 4.1 16.6 - - + -
282A ALA* 3.3 17.8 + - + +
283A ALA* 3.2 9.3 + - - +
285A ALA* 1.3 75.5 - - - +
287A ARG* 1.3 60.0 + - - +
289A ALA* 4.0 1.5 - - - +
290A ALA* 2.9 30.0 + - - +
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PRO* 3.8 21.7 - - + +
196A ARG* 3.6 33.2 - - - +
197A ALA* 3.0 31.5 + - - +
283A ALA 3.0 12.7 + - - +
284A GLU* 2.8 46.8 + - - +
286A ILE* 1.3 77.7 - - - +
288A VAL* 1.3 65.4 + - - +
290A ALA* 3.8 1.4 - - - +
291A LEU* 3.1 53.3 + - + +
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Residues in contact with VAL 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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187A PHE* 3.8 34.3 - - + +
191A ALA* 6.3 0.4 - - + -
197A ALA* 4.0 15.9 - - + -
200A VAL* 4.6 7.4 - - + -
214A LEU* 4.2 15.7 - - + -
216A LEU* 5.9 1.1 - - + -
284A GLU* 3.0 35.6 + - + +
285A ALA* 3.7 9.4 - - - +
287A ARG* 1.3 77.4 - - - +
289A ALA* 1.3 67.4 + - - +
291A LEU* 3.2 12.1 + - - +
292A LEU* 3.1 26.6 + - + +
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Residues in contact with ALA 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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179A ALA* 4.2 9.0 - - - +
180A THR* 3.4 35.4 + - + +
184A ILE* 4.2 11.2 - - + -
187A PHE* 4.7 4.5 - - + -
285A ALA 2.9 18.0 + - - +
286A ILE* 4.0 2.9 - - - +
288A VAL* 1.3 77.4 - - - +
290A ALA* 1.3 64.3 + - - +
292A LEU* 3.2 24.3 + - - +
293A ARG* 3.5 12.2 + - - +
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Residues in contact with ALA 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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105A LEU 4.1 1.6 - - - +
106A TRP* 4.1 11.5 - - + -
107A PRO* 3.7 25.1 - - + -
286A ILE 2.9 19.7 + - - +
287A ARG 3.8 2.9 - - - +
289A ALA* 1.3 78.8 - - - +
291A LEU* 1.3 63.0 + - - +
293A ARG* 3.1 44.9 + - - +
294A THR* 4.3 3.3 + - - -
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Residues in contact with LEU 291 (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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200A VAL* 4.3 27.6 - - + -
287A ARG* 3.1 46.8 + - + +
288A VAL* 3.5 10.8 - - - +
290A ALA* 1.3 75.1 - - - +
292A LEU* 1.3 61.1 + - + +
293A ARG 3.1 1.2 + - - -
294A THR* 3.2 7.1 + - - -
295A LEU* 2.9 34.6 + - + +
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Residues in contact with LEU 292 (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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179A ALA* 4.2 14.4 - - + -
187A PHE* 3.4 41.3 - - + -
200A VAL* 3.8 24.9 - - + -
202A VAL* 3.8 31.6 - - + -
205A ARG* 2.7 29.8 + - - -
210A ASN* 5.8 3.0 + - - +
223A TRP* 3.9 15.9 - - + -
288A VAL* 3.1 19.7 + - + +
289A ALA* 3.5 9.4 - - - +
290A ALA 3.2 0.4 - - - -
291A LEU* 1.3 79.6 - - - +
293A ARG* 1.3 55.7 + - - +
294A THR 3.2 0.4 - - - -
295A LEU* 4.2 6.5 - - + -
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Residues in contact with ARG 293 (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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105A LEU* 2.9 37.2 + - - +
106A TRP* 3.3 48.2 - - + -
172A GLU* 3.8 30.7 - - - +
176A GLY* 2.9 32.2 + - - +
180A THR* 2.9 34.3 + - - +
205A ARG* 4.2 8.4 + - - +
286A ILE 5.3 0.2 + - - -
289A ALA* 3.5 5.4 + - - +
290A ALA* 3.1 22.9 + - - +
292A LEU* 1.3 77.7 - - - +
294A THR* 1.3 68.8 + - + +
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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