Contacts of the helix formed by residues 284 - 296 (chain B) in PDB entry 3A7H
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 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B GLN* 4.4 18.8 - - + +
123B THR* 3.9 30.5 - - + -
124B ILE* 4.1 19.7 - - + -
152B LEU* 3.8 13.5 - - + -
156B GLY* 3.5 26.2 - - - +
158B VAL* 3.8 19.3 - - + -
280B LYS 5.0 0.2 - - - +
281B THR* 2.8 15.6 + - - +
283B TYR* 1.3 76.9 - - + +
285B THR* 1.3 63.6 + - - +
286B GLU 3.0 2.9 - - - -
287B LEU* 3.0 24.7 + - + +
288B ILE* 3.0 24.6 + - - +
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Residues in contact with THR 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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154B GLU 3.7 21.5 - - - +
155B HIS* 3.7 22.2 - - + +
281B THR 4.3 0.2 + - - -
282B SER* 3.0 22.0 + - - +
283B TYR* 4.5 1.0 - - - -
284B LEU* 1.3 78.7 - - - +
286B GLU* 1.3 55.3 + - - +
288B ILE* 3.6 8.5 - - - -
289B ASP* 2.7 50.0 + - - +
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Residues in contact with GLU 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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120B GLN* 5.5 5.4 - - - +
283B TYR 3.4 12.0 + - - +
284B LEU 3.0 1.0 - - - -
285B THR* 1.3 84.8 + - - +
287B LEU* 1.3 56.4 + - - +
289B ASP* 3.8 9.4 - - - +
290B ARG* 2.8 20.0 + - + +
293B ARG* 3.4 32.2 + - - -
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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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110B LEU* 3.8 30.7 - - + +
116B LEU* 3.5 35.7 - - + -
120B GLN* 3.7 29.0 - - - +
124B ILE* 4.0 18.4 - - + -
283B TYR 4.4 0.8 + - - -
284B LEU* 3.0 20.4 + - + +
286B GLU* 1.3 76.4 - - - +
288B ILE* 1.3 58.4 + - - +
290B ARG* 3.3 34.5 + - - +
291B TYR* 3.0 27.7 + - - +
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Residues in contact with ILE 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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103B GLY 5.4 0.2 - - - +
104B GLY* 3.9 29.4 - - - +
110B LEU* 3.9 19.5 - - + -
152B LEU* 4.3 9.9 - - + -
153B SER 3.1 27.1 - - - +
154B GLU* 3.9 18.6 - - + +
156B GLY* 3.5 24.0 - - - +
284B LEU 3.0 17.5 + - - +
285B THR* 3.6 7.0 - - - +
287B LEU* 1.3 73.2 - - - +
289B ASP* 1.3 65.3 + - - +
291B TYR* 3.2 5.5 + - - +
292B LYS* 2.9 32.2 + - + +
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Residues in contact with ASP 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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154B GLU 5.7 0.5 - - - +
285B THR* 2.7 37.2 + - - +
286B GLU* 3.7 18.0 - - - +
288B ILE* 1.3 74.1 - - - +
290B ARG* 1.3 66.9 + - - +
292B LYS* 3.5 9.7 - - - +
293B ARG* 2.9 37.8 + - + +
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Residues in contact with ARG 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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80A PRO* 5.9 5.6 - - - +
81A TYR* 5.9 2.1 + - - -
110B LEU 2.9 23.0 + - - -
113B PRO* 3.6 18.3 + - + +
114B GLY* 2.8 44.6 + - - +
115B PRO* 3.3 21.9 + - - +
116B LEU* 4.2 1.8 - - - +
286B GLU* 2.8 19.6 + - + +
287B LEU* 3.4 27.4 + - - +
288B ILE 3.2 0.2 - - - -
289B ASP* 1.3 76.1 - - - +
291B TYR* 1.3 58.5 + - - +
293B ARG* 3.3 25.7 + - - +
294B TRP* 2.9 29.7 + - - +
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Residues in contact with TYR 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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104B GLY 4.3 8.7 - - - -
105B GLY* 5.0 4.7 - - - -
109B ASP* 3.3 52.3 + - + +
110B LEU* 3.6 28.5 - - + -
112B GLU* 4.2 3.5 - - + +
113B PRO* 3.9 18.4 - - + +
287B LEU 3.0 6.7 + - - +
288B ILE 3.5 8.3 - - - +
290B ARG* 1.3 75.3 - - - +
292B LYS* 1.3 62.9 + - + +
294B TRP* 3.9 22.9 - + - -
295B LYS* 2.8 58.1 + - + +
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Residues in contact with LYS 292 (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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288B ILE* 2.9 18.4 + - + +
289B ASP* 3.1 14.6 + - - +
291B TYR* 1.3 76.0 - - + +
293B ARG* 1.3 68.9 + - + +
295B LYS* 3.6 6.6 + - - +
296B ALA* 3.2 19.1 + - - +
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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
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286B GLU* 3.4 25.1 + - - -
289B ASP* 2.9 26.9 + - + +
290B ARG* 3.5 31.6 - - - +
292B LYS* 1.3 78.9 - - + +
294B TRP* 1.3 66.6 + - - +
296B ALA* 2.7 26.3 + - - +
297B GLU* 3.8 9.5 - - - +
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Residues in contact with TRP 294 (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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130A LYS* 5.6 7.7 - - - +
112B GLU* 3.8 40.5 + - + -
113B PRO* 3.6 39.8 - - + +
290B ARG 2.9 18.3 + - - +
291B TYR* 3.6 22.4 - + - +
293B ARG* 1.3 75.8 - - - +
295B LYS* 1.3 78.4 + - + +
296B ALA 2.8 10.6 + - - -
297B GLU* 2.9 21.3 + - - +
298B GLN* 3.3 52.8 + - + +
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Residues in contact with LYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 2.8 50.8 + - + +
292B LYS* 3.8 7.0 - - - +
294B TRP* 1.3 88.1 - - + +
296B ALA* 1.3 55.7 + - - +
297B GLU 3.1 6.2 + - - -
298B GLN* 3.7 20.3 + - + +
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Residues in contact with ALA 296 (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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292B LYS* 3.2 12.4 + - + +
293B ARG* 2.7 17.2 + - - +
295B LYS* 1.3 75.1 - - - +
297B GLU* 1.3 70.5 + - - +
298B GLN 3.9 0.2 - - - -
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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