Contacts of the helix formed by residues 282 - 287 (chain A) in PDB entry 3GEB
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 PHE 282 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ASP* 3.4 11.3 + - - +
277A GLU* 3.2 6.9 + - - -
280A ILE* 4.0 11.8 - - + -
281A ILE* 1.3 76.2 - - - +
283A HIS* 1.3 102.7 + + - +
284A SER 3.3 0.9 - - - -
285A LEU* 3.1 27.3 + - + +
286A LEU* 3.8 12.4 + - + +
305A GLY 3.6 21.1 - - - -
308A MET* 3.8 8.7 - - + -
309A GLU* 3.7 33.0 - - + -
312A ILE* 3.8 17.7 - - + -
313A PHE* 5.8 2.2 - + - -
457A LYS* 3.8 22.9 - - - -
461A TYR* 3.6 17.7 - + - +
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Residues in contact with HIS 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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276A ASP* 3.1 31.6 + - + +
277A GLU* 3.4 7.7 + - - +
282A PHE* 1.3 101.9 - + - +
284A SER* 1.3 58.4 + - - +
285A LEU 3.0 4.7 - - - -
286A LEU* 3.0 33.2 + - + +
287A THR* 3.4 15.7 + - + +
449A THR* 4.9 5.8 - - - -
457A LYS* 4.2 7.2 + - - -
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Residues in contact with SER 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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277A GLU* 2.6 35.8 + - - +
281A ILE* 3.5 18.5 - - - +
283A HIS* 1.3 75.0 - - - +
285A LEU* 1.3 59.4 + - - +
286A LEU 3.4 0.2 - - - -
287A THR* 3.6 12.1 - - - -
288A GLY* 3.7 2.4 + - - -
289A THR* 3.2 25.1 + - - -
290A PHE* 3.3 30.0 + - - +
301A SER* 4.3 1.0 + - - -
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Residues in contact with LEU 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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281A ILE* 3.9 32.3 - - + +
282A PHE* 3.1 18.3 + - + +
283A HIS 3.0 0.4 + - - -
284A SER* 1.3 81.0 - - - +
286A LEU* 1.3 60.8 + - - +
288A GLY 4.0 2.6 + - - -
290A PHE* 5.0 2.7 - - + -
301A SER* 2.8 43.9 + - - +
302A VAL* 3.5 6.2 + - - +
304A ILE* 4.2 4.7 - - + +
305A GLY* 3.9 21.8 - - - +
308A MET* 5.8 0.9 - - + -
417A LEU* 3.3 30.3 - - + -
420A LEU* 3.4 33.9 - - + -
461A TYR* 4.7 1.6 - - - +
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Residues in contact with LEU 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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282A PHE* 3.9 21.5 - - + +
283A HIS* 3.0 20.6 + - + +
285A LEU* 1.3 79.5 - - - +
287A THR* 1.3 61.4 + - + +
288A GLY 3.5 0.2 - - - -
302A VAL* 4.0 10.1 - - - +
305A GLY* 3.3 37.9 - - - -
306A LEU* 3.4 17.7 - - + +
309A GLU* 3.9 24.2 - - - +
407B ARG* 4.7 7.6 - - - +
411B LEU* 3.7 43.0 - - + +
414B ARG* 5.5 0.2 - - - +
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Residues in contact with THR 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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283A HIS* 3.4 8.4 + - + +
284A SER* 3.6 10.2 - - - -
286A LEU* 1.3 80.4 - - + +
288A GLY* 1.3 62.5 + - - +
289A THR* 3.3 27.1 + - - +
411B LEU* 5.7 3.8 - - + -
414B ARG* 4.0 28.2 + - - +
415B ALA* 3.5 17.1 + - - +
418B GLU* 3.6 13.5 - - - +
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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
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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