Contacts of the helix formed by residues 284 - 297 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLN* 4.3 28.9 - - + +
123A THR* 3.6 37.5 - - + -
124A ILE* 4.1 11.0 - - + -
152A LEU* 3.9 13.7 - - + -
156A GLY* 3.5 25.4 - - - +
158A VAL* 3.9 19.1 - - + -
280A LYS 4.9 0.2 - - - +
281A THR* 2.7 14.3 + - - +
283A TYR* 1.3 79.6 - - + +
285A THR* 1.3 63.1 + - - -
286A GLU 3.2 0.4 - - - -
287A LEU* 3.2 17.5 + - + +
288A ILE* 3.0 24.1 + - - +
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Residues in contact with THR 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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154A GLU 4.1 4.5 - - - +
155A HIS* 3.5 34.1 - - + +
282A SER* 2.8 27.2 + - - +
283A TYR 3.2 0.5 + - - -
284A LEU* 1.3 77.4 - - - +
286A GLU* 1.3 55.5 + - - +
288A ILE* 3.0 11.8 + - - +
289A ASP* 2.6 46.7 + - - -
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Residues in contact with GLU 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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120A GLN* 5.3 6.5 - - - +
283A TYR 3.6 11.1 + - - +
284A LEU 3.2 0.2 - - - -
285A THR* 1.3 81.5 + - - +
287A LEU* 1.3 53.1 + - - +
289A ASP* 3.0 9.9 + - - +
290A ARG* 2.8 35.3 + - + +
293A ARG* 3.7 23.7 + - - -
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Residues in contact with LEU 287 (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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110A LEU* 3.7 33.9 - - + +
116A LEU* 3.4 36.1 - - + -
120A GLN* 3.4 36.2 - - + +
124A ILE* 4.2 16.2 - - + -
284A LEU* 3.2 19.1 + - + +
286A GLU* 1.3 79.5 - - - +
288A ILE* 1.3 62.0 + - - +
290A ARG* 3.4 33.5 + - - +
291A TYR* 3.3 15.9 + - - +
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Residues in contact with ILE 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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103A GLY 4.9 2.0 - - - +
104A GLY* 3.8 31.4 - - - +
110A LEU* 3.9 17.7 - - + -
152A LEU* 4.2 8.3 - - + -
153A SER 3.3 24.0 - - - +
154A GLU* 3.7 16.8 - - + +
156A GLY* 3.6 22.9 - - - +
284A LEU 3.0 21.7 + - - +
285A THR* 3.3 8.1 - - - +
287A LEU* 1.3 77.0 - - - +
289A ASP* 1.3 67.8 + - - +
291A TYR* 3.2 13.5 + - - +
292A LYS* 3.3 21.1 + - + +
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Residues in contact with ASP 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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285A THR* 2.6 31.9 + - - +
286A GLU* 3.0 10.5 + - - +
288A ILE* 1.3 75.2 - - - +
290A ARG* 1.3 65.2 + - - +
292A LYS* 3.2 11.2 + - - +
293A ARG* 3.0 41.6 + - + +
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Residues in contact with ARG 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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110A LEU 2.8 26.9 + - - -
113A PRO* 3.0 26.4 - - + +
114A GLY* 3.0 29.9 + - - +
115A PRO* 3.4 19.8 + - - +
116A LEU* 3.9 1.6 - - - +
286A GLU* 2.8 18.6 + - + +
287A LEU* 3.5 28.2 + - - +
288A ILE 3.2 0.2 - - - -
289A ASP* 1.3 77.3 - - - +
291A TYR* 1.3 57.5 + - - +
293A ARG* 3.5 28.5 + - - +
294A TRP* 3.0 28.3 + - + +
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Residues in contact with TYR 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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104A GLY 4.7 12.1 - - - -
105A GLY* 5.2 4.0 - - - -
109A ASP* 3.1 52.8 + - + +
110A LEU* 3.8 18.8 - - + -
112A GLU* 4.2 3.4 - - + -
113A PRO* 3.8 12.8 - - + +
287A LEU 3.3 2.7 + - - +
288A ILE 3.2 9.3 + - - +
289A ASP 3.1 0.6 - - - -
290A ARG* 1.3 78.6 - - - +
292A LYS* 1.3 67.6 + - + +
294A TRP* 3.6 29.9 - + - +
295A LYS* 2.9 72.8 + - + +
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Residues in contact with LYS 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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103A GLY 5.8 4.3 - - - +
288A ILE* 3.3 18.5 + - + +
289A ASP* 3.2 15.2 + - - +
291A TYR* 1.3 83.1 - - + +
293A ARG* 1.3 62.4 + - + +
295A LYS* 3.3 9.3 + - + +
296A ALA* 2.9 28.9 + - - +
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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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286A GLU* 3.7 21.4 + - - -
289A ASP* 3.0 29.5 + - + +
290A ARG* 3.6 32.4 + - - +
292A LYS* 1.3 78.9 - - + +
294A TRP* 1.3 62.5 + - - +
296A ALA* 3.2 20.1 + - - +
297A GLU* 3.4 14.9 + - - +
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Residues in contact with TRP 294 (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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112A GLU* 3.7 48.5 + - + -
113A PRO* 3.7 27.9 + - + +
290A ARG* 3.0 18.5 + - + +
291A TYR* 3.6 26.2 - + - +
293A ARG* 1.3 79.3 - - - +
295A LYS* 1.3 81.6 + - + +
297A GLU* 3.0 11.0 + - - +
298A GLN* 3.0 66.4 + - + +
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Residues in contact with LYS 295 (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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30A ILE 5.4 5.1 + - - -
109A ASP* 5.9 0.2 + - - -
291A TYR* 2.9 58.2 + - + +
292A LYS* 3.6 9.4 - - + +
294A TRP* 1.3 87.1 - - + +
296A ALA* 1.3 65.4 + - - +
297A GLU 3.1 0.7 + - - -
298A GLN* 3.2 20.5 + - + +
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Residues in contact with ALA 296 (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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292A LYS 2.9 14.8 + - - +
293A ARG* 3.4 13.7 - - - +
294A TRP 3.2 0.2 - - - -
295A LYS* 1.3 77.8 - - - +
297A GLU* 1.3 69.9 - - - +
298A GLN 3.6 5.2 + - - +
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Residues in contact with GLU 297 (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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293A ARG 3.7 11.9 - - - +
294A TRP* 3.0 11.4 + - + +
296A ALA* 1.3 88.8 - - - +
298A GLN* 1.3 72.6 + - - +
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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