Contacts of the helix formed by residues 363 - 373 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A HIS* 5.0 2.6 - - + -
361A VAL* 3.8 0.9 - - - +
362A GLU* 1.3 92.2 - - + +
364A LEU* 1.3 63.9 + - - +
365A GLU* 3.4 19.4 + - - +
366A GLU* 3.1 38.5 + - - +
367A TRP 3.0 17.2 + - - -
382A LEU* 3.6 13.3 - - - +
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Residues in contact with LEU 364 (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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147A PRO* 3.8 16.2 - - + +
150A TRP* 3.4 45.5 - - + +
151A MET* 4.5 1.6 - - - +
152A MET* 3.8 38.8 - - + +
363A THR* 1.3 71.7 - - - +
365A GLU* 1.3 74.1 + - - +
367A TRP* 3.1 17.5 + - + +
368A CYS* 2.9 31.0 + - - -
382A LEU* 4.1 9.3 - - + +
397A PRO* 4.7 1.1 - - + -
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Residues in contact with GLU 365 (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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147A PRO* 3.6 34.0 - - + +
333A HIS* 3.9 33.2 - - + +
363A THR* 3.4 21.7 - - - +
364A LEU* 1.3 83.6 + - - +
366A GLU* 1.3 61.3 + - - +
368A CYS* 3.5 0.3 + - - +
369A TRP* 3.3 30.6 + - + +
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Residues in contact with GLU 366 (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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329A VAL* 3.5 26.2 - - + +
330A ARG* 3.3 27.5 + - - -
331A ASP* 3.8 17.6 + - - +
332A ILE* 4.2 8.1 - - + +
333A HIS* 4.5 8.3 - - - +
361A VAL* 3.7 8.6 - - + -
362A GLU* 2.7 31.2 + - - +
363A THR* 3.1 31.1 + - - +
365A GLU* 1.3 77.0 - - - +
367A TRP* 1.3 62.7 + - - +
368A CYS 3.4 0.2 + - - -
369A TRP* 3.5 0.5 + - - -
370A LEU* 3.1 30.0 + - + +
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Residues in contact with TRP 367 (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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145A LEU* 4.8 7.6 - - + -
150A TRP* 3.5 53.4 - + - -
179A PRO* 3.8 15.9 - - + +
180A ALA* 5.7 0.9 - - - -
361A VAL* 4.0 7.8 - - + +
363A THR 3.0 12.8 + - - +
364A LEU* 3.1 13.6 + - + +
366A GLU* 1.3 75.0 - - - +
368A CYS* 1.3 76.4 + - - +
370A LEU* 3.4 4.1 + - - +
371A GLN* 2.8 58.1 + - + +
378A PHE* 3.4 23.5 - + - -
382A LEU* 4.2 13.7 - - + -
383A PHE* 3.4 21.8 - + - -
397A PRO* 3.7 32.8 - - + -
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Residues in contact with CYS 368 (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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141A LEU* 4.1 3.4 - - + +
145A LEU* 3.2 34.4 - - - +
146A GLN 4.1 1.3 - - - -
147A PRO* 3.7 29.8 - - + -
150A TRP* 4.2 8.3 - - - -
364A LEU* 2.9 25.0 + - - +
365A GLU 3.9 3.6 - - - +
366A GLU 3.3 0.2 - - - -
367A TRP* 1.3 96.9 - - - +
369A TRP* 1.3 61.0 + - + +
371A GLN* 3.2 6.6 + - - +
372A SER* 2.9 28.2 + - - -
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Residues in contact with TRP 369 (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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10A GLN* 4.7 1.6 - - - -
73A ASP* 3.9 28.8 + - + -
75A VAL* 3.6 16.6 - - + -
139A TYR* 3.4 28.5 - + + -
141A LEU* 3.6 39.0 - - + +
147A PRO* 5.4 3.7 - - + +
332A ILE* 4.2 19.5 - - + +
333A HIS* 3.2 38.1 + - + +
339A GLN* 3.3 36.6 - - + -
365A GLU* 3.3 19.9 + - - +
368A CYS* 1.3 77.8 - - + +
370A LEU* 1.3 59.9 + - - +
372A SER* 2.8 29.3 + - - -
373A VAL* 3.1 22.7 + - + +
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Residues in contact with LEU 370 (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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324A VAL* 5.9 0.4 - - + -
329A VAL* 3.9 22.2 - - + -
332A ILE* 3.7 27.6 - - + -
342A VAL* 3.9 6.5 - - + -
358A ALA* 3.8 21.5 - - + -
361A VAL* 3.8 19.3 - - + -
366A GLU 3.1 23.5 + - - +
367A TRP 3.7 0.2 - - - +
369A TRP* 1.3 74.6 - - - +
371A GLN* 1.3 63.1 + - - +
373A VAL* 3.2 11.6 - - - +
375A ILE* 3.0 49.7 + - + +
378A PHE* 3.5 16.8 - - + -
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Residues in contact with GLN 371 (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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145A LEU* 3.8 26.6 - - + +
179A PRO* 5.4 1.4 - - - +
180A ALA* 4.7 12.4 + - - +
367A TRP* 2.8 51.6 + - + +
368A CYS* 3.4 6.7 - - - +
370A LEU* 1.3 76.3 - - - +
372A SER* 1.3 61.4 + - - +
374A GLY* 3.2 4.3 + - - -
375A ILE 3.7 7.0 - - - -
376A ARG* 3.1 61.7 + - - +
378A PHE* 3.4 10.7 - - - -
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Residues in contact with SER 372 (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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139A TYR* 6.0 0.7 - - - -
140A CYS 5.6 0.4 - - - -
141A LEU* 3.6 20.1 - - - +
142A PRO* 4.2 10.5 - - - -
145A LEU* 3.9 16.1 - - - +
368A CYS 2.9 12.4 + - - -
369A TRP* 2.8 31.2 + - - -
370A LEU 3.2 0.2 - - - -
371A GLN* 1.3 78.1 - - - +
373A VAL* 1.3 60.8 + - - +
374A GLY* 3.3 1.2 + - - -
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Residues in contact with VAL 373 (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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139A TYR* 4.2 20.4 - - + -
332A ILE* 5.1 1.8 - - + -
339A GLN* 4.3 17.9 - - + +
342A VAL* 3.8 25.8 - - + -
343A ALA* 3.8 27.7 - - + +
346A VAL* 3.6 21.3 - - + +
369A TRP* 3.1 16.3 + - + +
370A LEU* 3.2 20.9 - - + +
372A SER* 1.3 80.1 - - - +
374A GLY* 1.3 57.1 + - - +
375A ILE* 4.7 0.4 - - + +
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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