Contacts of the helix formed by residues 284 - 292 (chain T) in PDB entry 5GJQ
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 284 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282T ILE 4.7 0.4 - - - -
283T LEU* 1.3 67.0 - - - +
285T THR* 1.3 63.5 + - - +
287T ALA* 3.0 10.4 + - + +
288T THR* 2.9 22.5 + - - -
296T PRO* 4.3 11.0 - - + -
299T MET* 3.6 31.8 - - + +
313T ASN* 2.4 48.4 + - + +
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Residues in contact with THR 285 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283T LEU* 4.3 7.3 - - - +
284T PHE* 1.3 77.9 - - - +
286T GLU* 1.3 67.7 + - - +
288T THR* 3.4 10.5 - - - -
289T ARG* 2.9 24.9 + - - +
313T ASN* 4.5 2.2 - - - -
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Residues in contact with GLU 286 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453S HIS* 6.3 4.3 - - + -
279T TYR* 5.9 1.3 - - - +
282T ILE* 4.8 9.0 - - + -
283T LEU* 2.8 34.7 + - + +
285T THR* 1.3 82.6 - - - +
287T ALA* 1.3 57.2 + - - +
289T ARG* 3.0 10.9 + - + +
290T ILE* 2.9 35.6 + - + +
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Residues in contact with ALA 287 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282T ILE* 4.8 15.1 - - + +
283T LEU 3.2 5.9 + - - +
284T PHE* 3.0 12.7 + - - +
286T GLU* 1.3 78.9 - - - +
288T THR* 1.3 61.9 + - - +
290T ILE* 3.1 7.8 + - - +
291T LEU* 2.9 40.5 + - + +
293T PHE* 5.3 1.3 - - - -
299T MET* 5.0 11.2 - - + -
308T TRP* 5.9 5.8 - - + -
315T TYR* 5.9 2.2 - - + -
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Residues in contact with THR 288 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284T PHE* 2.9 13.1 + - - -
285T THR* 3.4 13.0 - - - -
287T ALA* 1.3 73.9 - - - +
289T ARG* 1.3 63.8 + - - +
292T PHE* 3.2 19.2 + - - -
293T PHE* 3.2 42.7 + - - +
294T ASN 5.3 0.3 - - - -
295T THR 3.9 13.3 + - - -
296T PRO* 5.5 3.8 - - - -
299T MET* 5.3 3.4 - - - +
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Residues in contact with ARG 289 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285T THR 2.9 15.3 + - - +
286T GLU* 3.2 13.5 - - - +
288T THR* 1.3 78.0 - - - +
290T ILE* 1.3 63.5 + - + +
292T PHE* 3.9 5.0 + - - -
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Residues in contact with ILE 290 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432S GLU* 6.0 6.3 - - + -
435S GLU* 6.2 0.2 - - - +
453S HIS* 6.2 0.9 - - - +
271T ILE* 3.9 26.5 - - + +
275T ILE* 6.5 1.3 - - + -
279T TYR* 4.7 14.4 - - - +
286T GLU* 2.9 22.4 + - + +
287T ALA* 3.1 7.6 + - - +
289T ARG* 1.3 80.4 - - + +
291T LEU* 1.3 71.3 + - + +
292T PHE* 3.1 7.9 + - - +
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Residues in contact with LEU 291 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268T ARG* 2.6 54.5 + - + +
271T ILE* 3.6 39.0 - - + -
272T ALA* 4.5 6.5 - - + +
275T ILE* 5.9 1.3 - - + -
287T ALA* 2.9 25.1 + - + +
290T ILE* 1.3 78.3 - - + +
292T PHE* 1.3 62.3 + - - +
293T PHE* 3.3 34.3 - - + -
299T MET* 6.1 0.2 - - - -
302T TYR* 4.6 14.4 - - + -
308T TRP* 5.3 14.4 - - + -
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Residues in contact with PHE 292 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244T VAL* 5.3 14.1 - - + -
268T ARG* 3.0 18.3 + - - +
288T THR 3.2 7.0 + - - -
289T ARG 3.9 3.6 + - - -
290T ILE 3.1 8.3 - - - +
291T LEU* 1.3 80.9 - - - +
293T PHE* 1.3 64.3 + - - +
294T ASN* 3.8 7.7 + - - +
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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