Contacts of the helix formed by residues 277 - 281 (chain G) in PDB entry 3ECS
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 277 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213G ASN* 5.0 0.4 + - - -
241G LEU 5.7 0.7 - - - +
275G TYR* 3.2 24.4 + - + +
276G THR* 1.3 79.5 - - - +
278G PRO* 1.3 76.5 - - + +
279G SER* 3.2 13.9 - - - +
280G LEU* 3.1 30.2 + - + +
281G ILE* 3.9 2.3 + - - +
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Residues in contact with PRO 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203G ASN* 3.1 42.6 - - + +
204G GLY 3.8 4.5 - - - +
205G GLY* 3.9 9.4 - - - -
275G TYR* 3.3 14.4 - - - +
276G THR 3.7 0.4 - - - -
277G ALA* 1.3 82.9 - - + +
279G SER* 1.3 56.8 + - - +
280G LEU 3.0 5.8 - - - -
281G ILE* 3.0 27.0 + - + +
293G PRO* 3.4 28.2 - - + +
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Residues in contact with SER 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G LYS* 3.1 24.3 + - - +
277G ALA* 4.1 12.3 - - - +
278G PRO* 1.3 79.9 - - - +
280G LEU* 1.3 61.1 + - - +
281G ILE 3.3 3.6 + - - +
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Residues in contact with LEU 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G ASN* 4.2 8.7 - - - +
216G ALA* 4.0 12.4 - - + +
217G VAL* 4.0 42.4 - - + -
220G LYS* 3.8 30.7 - - + +
226G PHE* 3.5 24.4 - - - +
276G THR* 3.9 15.3 - - + -
277G ALA* 3.1 30.0 + - + +
278G PRO 3.0 1.4 - - - -
279G SER* 1.3 83.3 - - - +
281G ILE* 1.3 61.1 + - - +
282G THR* 5.1 0.6 + - - -
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Residues in contact with ILE 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204G GLY 3.6 14.8 - - - +
205G GLY* 4.3 5.8 - - - -
206G ILE* 3.5 37.9 - - + +
220G LYS* 6.4 0.2 - - - -
226G PHE* 4.1 16.6 - - + +
228G VAL* 4.0 13.0 - - + -
276G THR* 4.3 4.9 - - + +
277G ALA 4.0 9.2 - - - +
278G PRO 3.0 10.1 + - - +
279G SER 3.3 2.3 - - - -
280G LEU* 1.3 84.1 - - - +
282G THR* 1.3 62.3 + - - +
283G LEU 3.8 20.6 - - - +
284G LEU* 4.0 7.0 - - + -
293G PRO* 3.3 29.7 - - + +
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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