Contacts of the helix formed by residues 281 - 286 (chain G) in PDB entry 4U7B
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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G THR* 6.0 0.2 - - - +
156G ASP* 5.0 5.2 - - - +
247G LEU* 5.0 6.3 - - + -
249G ALA* 6.6 0.2 - - + -
273G HIS* 3.9 20.0 - - + +
278G PRO* 3.0 14.2 + - + +
279G ASP 3.5 0.6 - - - -
280G LEU* 1.3 77.6 - - - +
282G PRO* 1.3 58.3 - - - +
283G SER* 3.1 3.1 - - - +
284G ASP* 2.7 44.5 + - + +
285G TYR* 3.1 13.5 + - - -
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Residues in contact with PRO 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G ILE* 6.0 0.7 - - + -
154G THR* 4.0 17.0 - - + +
197G TRP* 3.4 26.0 - - + -
247G LEU* 4.7 8.7 - - + -
280G LEU 3.4 10.5 - - - +
281G ALA* 1.3 82.0 - - - +
283G SER* 1.3 63.6 + - - +
285G TYR* 3.6 18.1 - - + +
286G HIS* 3.0 26.9 + - - +
287G LEU 3.4 2.4 + - - -
325G GLY 4.4 2.2 - - - +
326G ILE* 4.0 13.7 - - + -
329G LEU* 3.5 31.0 - - + -
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Residues in contact with SER 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G THR* 3.6 6.4 + - - +
155G GLY* 3.6 21.9 + - - -
156G ASP* 3.6 28.0 - - - -
195G VAL* 5.5 0.4 - - - -
197G TRP* 3.2 28.1 + - - +
281G ALA* 3.0 2.5 + - - -
282G PRO* 1.3 76.2 - - - +
284G ASP* 1.3 57.5 + - - +
287G LEU* 3.7 2.8 - - - +
288G PHE* 2.9 44.7 + - - -
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Residues in contact with ASP 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G ASP* 3.4 25.0 - - - +
157G GLU 5.1 1.0 - - - +
278G PRO* 3.4 35.8 - - + +
281G ALA* 2.7 20.3 + - - +
283G SER* 1.3 74.9 - - - +
285G TYR* 1.3 62.0 + - - +
286G HIS 3.5 0.3 + - - -
288G PHE* 3.5 21.2 - - - +
289G ALA* 3.5 16.5 + - - +
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Residues in contact with TYR 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G PRO 4.0 5.2 - - - +
279G ASP* 3.6 9.0 - - - -
280G LEU* 4.0 4.9 - - - -
281G ALA 3.1 24.6 + - - -
282G PRO* 3.6 19.0 - - + +
284G ASP* 1.3 77.8 - - - +
286G HIS* 1.3 77.7 + + + +
289G ALA* 3.1 16.1 - - - +
325G GLY 2.8 23.0 + - - -
328G LYS* 3.7 24.1 + - + +
329G LEU* 2.8 23.9 + - + +
332G ARG* 3.2 51.9 + - + +
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Residues in contact with HIS 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G TRP* 4.5 7.1 - - + -
282G PRO* 3.0 14.2 + - + +
284G ASP 3.4 0.2 - - - -
285G TYR* 1.3 90.2 - - + +
287G LEU* 1.3 77.0 + - - +
288G PHE 3.4 1.1 - - - -
289G ALA* 3.0 12.5 + - - +
290G SER* 3.0 15.1 + - - -
321G PHE* 3.0 65.4 + + - -
322G TYR* 4.6 1.3 - - - -
324G ARG* 4.4 7.3 + - - +
325G GLY* 3.2 27.3 + - - -
328G LYS* 3.8 25.5 + - - +
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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