Contacts of the helix formed by residues 363 - 373 (chain B) in PDB entry 3GG0
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 THR 363 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333B HIS* 5.7 1.7 + - - -
361B VAL* 4.1 0.7 - - - +
362B GLU* 1.3 89.5 - - + +
364B LEU* 1.3 65.0 + - - +
365B GLU* 3.6 16.0 - - - +
366B GLU* 3.1 40.4 + - - +
367B TRP 3.2 8.8 + - - -
382B LEU* 3.5 10.6 - - - +
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Residues in contact with LEU 364 (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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147B PRO* 4.8 15.0 - - + +
150B TRP* 3.8 31.2 - - + +
151B MET* 4.0 21.8 - - + +
152B MET* 3.8 36.3 - - + +
363B THR* 1.3 71.6 - - - +
365B GLU* 1.3 56.2 + - - +
367B TRP* 3.4 12.4 + - + +
368B CYS* 2.9 36.8 + - - -
382B LEU* 3.8 11.6 - - + +
397B PRO* 4.0 9.9 - - + -
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Residues in contact with GLU 365 (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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147B PRO* 4.1 28.6 - - + +
333B HIS* 3.2 44.0 + - + +
363B THR* 3.6 14.5 + - - +
364B LEU* 1.3 78.5 - - - +
366B GLU* 1.3 63.1 + - - +
368B CYS* 3.3 2.1 + - - +
369B TRP* 3.0 34.4 + - + +
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Residues in contact with GLU 366 (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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329B VAL* 3.5 29.8 - - + +
330B ARG* 3.1 27.2 + - - -
331B ASP* 3.9 13.8 + - - +
332B ILE* 4.2 12.3 - - + +
333B HIS* 5.1 7.0 + - + +
361B VAL* 3.6 6.9 - - + -
362B GLU* 2.8 30.2 + - - +
363B THR* 3.1 23.8 + - - +
365B GLU* 1.3 75.2 - - - +
367B TRP* 1.3 66.7 + - - +
369B TRP* 3.3 1.2 + - - +
370B LEU* 2.9 31.8 + - + +
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Residues in contact with TRP 367 (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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145B LEU* 4.8 5.6 - - + -
150B TRP* 3.7 57.9 - + - -
179B PRO* 3.5 26.3 - - + +
180B ALA* 5.8 0.7 - - - -
361B VAL* 4.1 7.9 - - + +
363B THR 3.2 9.8 + - - +
364B LEU* 3.7 17.0 - - + +
366B GLU* 1.3 76.9 - - - +
368B CYS* 1.3 81.1 + - - +
370B LEU* 3.9 0.7 - - - +
371B GLN* 3.0 48.7 + - + +
378B PHE* 3.3 45.5 - + - -
382B LEU* 4.1 13.2 - - + -
383B PHE* 3.7 16.2 - + - -
397B PRO* 4.1 13.5 - - + -
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Residues in contact with CYS 368 (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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141B LEU* 4.1 4.2 - - + +
145B LEU* 3.3 37.8 - - - +
146B GLN 4.2 0.7 - - - -
147B PRO* 3.9 24.7 - - + -
150B TRP* 4.2 4.5 - - - -
364B LEU* 2.9 25.3 + - - +
365B GLU* 3.5 7.0 - - - +
367B TRP* 1.3 100.4 - - - +
369B TRP* 1.3 65.1 + - + +
371B GLN* 3.8 3.9 - - - +
372B SER* 3.1 23.6 + - - -
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Residues in contact with TRP 369 (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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73B ASP* 3.8 34.8 + - + -
75B VAL* 3.7 18.4 - - + -
139B TYR* 3.6 26.2 - + + -
141B LEU* 3.7 38.9 - - + +
147B PRO* 5.5 2.1 - - + +
332B ILE* 4.1 21.3 - - + +
333B HIS* 3.3 38.6 - - + +
339B GLN* 3.3 29.6 - - + -
365B GLU* 3.0 35.0 + - + +
368B CYS* 1.3 75.7 - - + +
370B LEU* 1.3 64.5 + - - +
372B SER* 2.9 26.2 + - - -
373B VAL* 3.3 17.4 + - + +
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Residues in contact with LEU 370 (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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324B VAL* 5.9 0.7 - - + -
329B VAL* 3.7 34.3 - - + -
332B ILE* 3.7 27.8 - - + -
342B VAL* 3.9 11.2 - - + -
358B ALA* 3.7 22.9 - - + -
361B VAL* 3.8 11.4 - - + -
366B GLU 2.9 21.9 + - - +
369B TRP* 1.3 74.8 - - - +
371B GLN* 1.3 63.8 + - - +
373B VAL* 3.2 15.6 - - - +
375B ILE* 3.0 40.3 + - + +
378B PHE* 3.7 13.9 - - + -
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Residues in contact with GLN 371 (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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145B LEU* 3.6 27.6 - - + +
179B PRO* 6.1 1.0 - - - +
180B ALA* 4.5 16.6 - - - +
367B TRP* 3.0 37.6 + - + +
368B CYS 3.8 4.0 - - - +
370B LEU* 1.3 77.3 - - - +
372B SER* 1.3 62.0 + - - +
374B GLY* 3.1 4.7 + - - -
375B ILE 3.4 15.5 - - - +
376B ARG* 2.8 62.3 + - - +
378B PHE* 3.8 14.2 - - + -
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.7 19.3 - - - +
142B PRO* 4.2 10.5 - - - -
145B LEU* 3.8 19.9 - - - +
368B CYS 3.1 15.5 + - - -
369B TRP* 2.9 19.8 + - - -
371B GLN* 1.3 77.8 - - - +
373B VAL* 1.3 65.1 + - - +
374B GLY* 3.3 1.1 + - - -
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Residues in contact with VAL 373 (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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139B TYR* 4.2 28.0 - - + -
332B ILE* 5.1 3.4 - - + -
339B GLN* 4.5 12.8 - - + +
342B VAL* 3.9 26.5 - - + -
343B ALA* 3.9 20.8 - - + +
346B VAL* 3.5 18.7 - - - +
369B TRP* 3.5 16.8 - - + +
370B LEU* 3.2 19.7 - - + +
372B SER* 1.3 82.4 - - - +
374B GLY* 1.3 55.7 + - - +
375B ILE* 4.5 1.6 - - + -
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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