Contacts of the helix formed by residues 280 - 291 (chain B) in PDB entry 5GT8
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 ILE 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B ILE* 4.2 13.9 - - + +
279B GLY* 1.3 74.3 - - - +
281B VAL* 1.3 62.4 + - - +
282B ALA* 2.9 9.3 + - - +
283B GLN* 2.9 37.0 + - + +
284B ILE* 3.1 12.8 - - - +
304B ASP* 3.5 5.6 + - - -
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 4.1 7.0 - - + -
112B VAL* 4.3 23.3 - - + +
114B MET* 4.8 18.4 - - + -
279B GLY 3.6 2.0 - - - -
280B ILE* 1.3 75.8 - - - +
282B ALA* 1.3 57.0 + - - +
284B ILE* 3.3 12.6 + - - +
285B ALA* 2.9 31.3 + - + +
297B TYR* 5.1 8.4 - - + -
299B SER* 5.0 4.5 - - - +
304B ASP* 4.1 12.8 + - + +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 6.5 0.2 - - - -
102B ILE* 3.7 20.8 - - + +
103B ALA* 5.0 3.1 - - + -
106B ALA* 3.7 30.1 - - + -
112B VAL* 5.5 0.6 - - - +
280B ILE* 2.9 2.6 + - - -
281B VAL* 1.3 79.4 - - - +
283B GLN* 1.3 65.6 + - + +
285B ALA 4.6 0.2 - - - +
286B GLY* 2.9 26.7 + - - +
287B PRO* 4.0 0.7 - - - +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B ILE* 4.5 8.5 - - + +
280B ILE* 2.9 29.8 + - + +
282B ALA* 1.3 77.6 - - + +
284B ILE* 1.3 60.5 + - + +
287B PRO* 3.0 24.1 - - - +
320B LEU* 5.8 1.7 - - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B VAL* 5.8 8.3 - - + -
268B ILE* 3.7 37.9 - - + -
280B ILE 3.1 22.0 - - - +
281B VAL* 3.3 11.9 + - - +
282B ALA 3.0 0.6 - - - -
283B GLN* 1.3 78.4 - - + +
285B ALA* 1.3 66.4 + - - +
286B GLY 3.0 3.3 + - - -
287B PRO* 3.1 12.1 - - - +
288B LEU* 3.2 39.7 - - + +
297B TYR* 4.2 6.3 - - + -
304B ASP* 5.4 5.4 - - + -
306B ALA* 3.8 23.3 - - + -
320B LEU* 6.4 3.4 - - + -
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 5.6 0.7 - - + -
98B ALA* 3.2 16.2 - - + +
102B ILE* 4.1 18.6 - - + -
281B VAL* 2.9 21.0 + - + +
282B ALA* 4.6 0.4 - - - +
284B ILE* 1.3 72.7 - - - +
286B GLY* 1.3 56.0 + - - +
288B LEU* 4.5 0.9 - - - -
289B ALA* 3.0 33.3 + - - +
297B TYR* 3.3 35.7 + - + +
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Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA* 4.2 8.7 - - - +
103B ALA* 6.1 4.0 - - - -
282B ALA* 2.9 16.1 + - - +
284B ILE 3.0 1.4 + - - -
285B ALA* 1.3 79.5 - - - +
287B PRO* 1.3 62.3 - - - +
289B ALA* 3.6 2.6 - - - +
290B ALA* 2.9 25.7 + - - +
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Residues in contact with PRO 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B ALA 4.0 0.7 - - - +
283B GLN* 3.0 30.3 - - - +
284B ILE* 3.1 10.8 - - - +
286B GLY* 1.3 84.6 - - - +
288B LEU* 1.3 62.9 + - + +
290B ALA* 3.3 12.1 - - + +
291B ALA* 3.3 19.4 + - - +
319B VAL* 3.9 30.3 - - + +
320B LEU* 4.9 8.1 - - + -
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B VAL* 6.4 0.2 - - + -
284B ILE* 3.2 40.1 + - + +
286B GLY 3.2 1.0 - - - -
287B PRO* 1.3 79.9 - - + +
289B ALA* 1.3 64.7 + - - +
290B ALA 3.1 1.3 - - - -
291B ALA* 3.1 6.1 + - + +
292B ASP 3.1 17.3 + - - -
293B ILE* 3.2 24.4 + - + +
295B ALA* 4.5 4.9 - - + -
297B TYR* 4.3 15.3 - - - +
306B ALA* 4.8 3.1 - - + -
308B VAL* 4.2 15.9 - - + -
316B VAL* 3.6 47.6 - - + +
319B VAL* 4.3 8.7 - - + -
320B LEU* 5.3 4.3 - - + +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS 4.3 20.0 + - - +
98B ALA* 3.7 17.5 - - + +
99B ARG* 3.3 28.2 + - + +
285B ALA 3.0 21.6 + - - +
286B GLY* 3.6 3.8 - - - +
288B LEU* 1.3 74.8 - - - +
290B ALA* 1.3 62.7 + - - +
292B ASP* 3.2 16.3 + - - +
293B ILE 5.1 2.5 - - - +
297B TYR* 5.1 2.1 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 4.4 11.3 + - - +
286B GLY 2.9 12.6 + - - +
287B PRO* 3.3 16.8 - - + +
288B LEU 3.1 0.2 - - - -
289B ALA* 1.3 78.7 - - - +
291B ALA* 1.3 58.3 + - - +
292B ASP* 3.5 7.8 + - - +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B PRO 3.3 9.3 + - - +
288B LEU* 3.1 11.7 + - + +
290B ALA* 1.3 76.9 - - - +
292B ASP* 1.3 72.4 + - - +
293B ILE* 3.3 9.5 + - + +
315B SER 5.9 2.0 - - - +
319B VAL* 5.2 9.6 - - + -
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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