Contacts of the helix formed by residues 281 - 286 (chain A) in PDB entry 3HOT
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 ALA 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A THR* 6.0 0.2 - - - +
156A ASP* 6.4 1.3 - - + -
247A LEU* 5.1 4.0 - - + -
249A ASP* 5.9 4.7 - - + +
273A HIS* 4.2 18.4 - - + +
278A PRO* 2.8 16.0 + - + +
279A ASP 3.5 0.8 - - - -
280A LEU* 1.3 79.3 - - - +
282A PRO* 1.3 70.6 - - + +
283A SER* 3.2 4.5 - - - +
284A ASP* 2.8 29.7 + - - +
285A TYR* 3.1 12.8 + - - -
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Residues in contact with PRO 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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152A ILE* 5.9 0.4 - - + -
154A THR* 4.0 11.9 - - + +
197A TRP* 3.6 25.3 - - + -
247A LEU* 3.6 23.6 - - + -
280A LEU 3.5 9.4 - - - +
281A ALA* 1.3 82.2 - - + -
283A SER* 1.3 63.6 + - - +
285A TYR* 3.1 18.6 - - + +
286A HIS* 2.9 23.8 + - + +
287A LEU 3.2 6.2 + - - -
325A GLY 4.9 1.6 - - - +
326A ILE* 4.1 7.0 - - + -
329A LEU* 3.1 27.1 - - + -
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Residues in contact with SER 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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154A THR* 3.6 13.2 + - - +
155A GLY 3.6 13.5 + - - -
156A ASP* 3.8 26.0 - - - -
195A VAL* 5.5 0.7 - - - -
197A TRP* 3.3 28.3 + - - +
281A ALA* 3.1 3.6 + - - +
282A PRO* 1.3 77.7 - - - +
284A ASP* 1.3 58.4 + - - +
287A LEU* 3.5 3.4 - - - +
288A PHE* 2.8 44.5 + - - -
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Residues in contact with ASP 284 (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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156A ASP* 3.2 27.2 - - - +
157A GLU 5.4 0.2 - - - +
249A ASP* 5.2 2.4 - - - +
278A PRO* 3.5 30.3 - - + +
281A ALA* 2.8 17.8 + - - +
283A SER* 1.3 78.5 - - - +
285A TYR* 1.3 64.1 + - - +
286A HIS 3.4 0.5 + - - -
288A PHE* 3.4 16.3 - - - +
289A ALA 3.5 8.0 + - - -
55F G 3.2 23.2 + - + +
56F A 3.7 32.2 + - - +
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Residues in contact with TYR 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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278A PRO 3.8 2.2 - - - +
279A ASP* 3.7 3.8 - - - -
280A LEU 3.7 5.2 - - - -
281A ALA 3.1 32.3 + - - -
282A PRO* 3.1 24.3 - - + +
284A ASP* 1.3 78.3 - - - +
286A HIS* 1.3 72.4 + - + +
289A ALA* 3.3 13.7 - - - +
325A GLY 3.2 14.0 + - - -
328A LYS* 4.2 13.7 - - + -
329A LEU* 2.9 34.5 + - + +
332A ARG* 3.0 52.7 - - - +
4E G 4.1 8.8 + + - +
55F G 3.3 23.7 + - - +
56F A 4.0 10.1 - - + -
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Residues in contact with HIS 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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197A TRP* 4.5 9.2 - + - -
282A PRO 2.9 13.2 + - - +
285A TYR* 1.3 98.2 - - + +
287A LEU* 1.3 69.6 + - - +
288A PHE 3.6 0.7 - - - -
289A ALA* 3.9 1.9 - - - +
290A SER* 3.4 17.3 + - - -
321A PHE* 2.8 47.8 + + - -
324A ARG* 3.2 28.7 - - - -
325A GLY* 3.4 24.1 - - - -
328A LYS* 3.3 20.4 + - - +
4E G 3.7 16.3 + - - +
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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