Contacts of the helix formed by residues 391 - 399 (chain A) in PDB entry 3QJT
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 SER 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A LEU 4.6 1.0 + - - -
352A GLY* 4.1 9.0 + - - -
355A GLY* 4.5 7.3 - - - -
386A HIS 3.0 8.0 + - - -
387A LEU* 3.0 24.3 + - - +
389A VAL 3.0 2.2 - - - +
390A ALA* 1.3 78.7 - - - +
392A LEU* 1.3 60.3 + - - +
395A LEU* 2.7 47.4 + - - +
428A TRP* 4.2 5.8 - - - +
429A PHE* 5.0 3.5 - - - -
432A MET* 4.3 17.9 - - - +
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Residues in contact with LEU 392 (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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240A LEU* 3.5 24.0 - - + -
243A ALA* 5.0 3.4 - - + -
244A TYR* 4.5 7.9 - - + -
247A ILE* 4.1 5.6 - - + -
349A PRO 3.9 3.6 - - - +
352A GLY* 3.2 42.0 - - - +
353A LEU* 3.5 24.5 - - + +
356A PHE* 3.4 32.5 - - + -
387A LEU 3.7 1.5 + - - +
388A GLN 3.5 12.5 + - - +
391A SER* 1.3 76.8 + - - +
393A VAL* 1.3 69.6 + - - +
396A THR* 2.7 38.1 + - - +
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Residues in contact with VAL 393 (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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80A PHE* 4.7 4.9 - - + -
81A THR* 3.8 24.0 - - + -
84A PHE* 4.9 14.9 - - + -
239A TRP* 2.9 37.0 - - + +
240A LEU* 3.8 18.6 - - + +
243A ALA* 4.4 9.6 - - + -
388A GLN 3.4 12.4 + - - +
389A VAL* 3.8 17.7 - - + +
392A LEU* 1.3 77.1 - - - +
394A THR* 1.3 65.0 + - - +
396A THR* 3.5 2.4 + - - -
397A ALA* 3.0 19.4 + - - +
801A HAS 4.3 1.1 - - + -
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Residues in contact with THR 394 (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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32A LEU* 3.8 11.0 - - + -
80A PHE* 3.0 27.7 - - + -
389A VAL 3.2 11.6 + - - -
390A ALA 3.0 26.0 - - - +
391A SER 3.8 0.4 + - - -
392A LEU 3.2 0.6 - - - -
393A VAL* 1.3 77.6 - - - +
395A LEU* 1.3 57.0 + - - +
397A ALA* 2.8 5.7 + - - +
398A MET* 2.8 59.1 + - + -
428A TRP* 4.0 4.7 - - + -
800A HEM 3.4 11.3 - - - +
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Residues in contact with LEU 395 (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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348A ALA* 3.1 35.4 - - + +
351A LEU* 4.1 12.3 - - + -
352A GLY* 4.0 13.5 - - - +
391A SER* 2.7 35.4 + - - +
392A LEU 4.0 0.4 - - - +
394A THR* 1.3 72.1 - - - +
396A THR* 1.3 54.9 + - - +
398A MET* 4.3 12.6 - - + -
399A GLY 2.7 30.7 + - - -
425A VAL* 4.2 20.4 - - + -
428A TRP* 3.6 43.1 - - + -
429A PHE* 4.5 11.4 - - + -
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Residues in contact with THR 396 (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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84A PHE* 4.2 3.6 - - + -
243A ALA* 3.3 42.3 - - + +
246A ILE* 4.1 24.4 - - + +
247A ILE* 4.2 1.0 - - - +
348A ALA* 4.2 1.0 + - - -
349A PRO* 3.4 30.7 - - + +
392A LEU* 2.7 29.9 + - - +
393A VAL 3.7 1.6 - - - -
395A LEU* 1.3 73.3 - - - +
397A ALA* 1.3 59.2 + - - +
399A GLY* 4.2 0.9 - - - -
400A SER* 3.3 20.8 + - - -
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Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.1 26.6 - - + -
80A PHE* 3.6 15.5 - - + -
84A PHE* 3.4 28.7 - - + -
393A VAL 3.0 12.4 + - - +
394A THR 2.8 15.3 + - - +
396A THR* 1.3 69.4 - - - +
398A MET* 1.3 58.5 + - - +
400A SER* 2.8 27.7 + - - -
401A LEU 3.7 1.7 + - - -
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Residues in contact with MET 398 (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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29A PHE* 3.4 12.3 - - + -
32A LEU* 4.4 13.9 - - + -
348A ALA* 5.3 0.7 - - + -
394A THR* 2.8 33.7 + - + +
395A LEU* 3.8 17.7 - - + +
397A ALA* 1.3 70.5 - - - +
399A GLY* 1.3 63.2 + - - +
401A LEU* 3.0 28.4 + - - +
402A TYR* 4.1 4.3 - - - -
424A VAL* 4.7 9.2 - - + -
425A VAL* 5.4 6.1 - - + -
428A TRP* 3.2 53.8 - - + -
481A LEU* 6.0 0.7 - - + -
484A PHE* 3.7 38.8 - - + -
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Residues in contact with GLY 399 (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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344A PRO 3.9 7.9 - - - -
345A ALA* 3.6 18.2 - - - -
348A ALA* 3.6 17.7 - - - +
349A PRO* 5.5 0.7 - - - -
395A LEU 2.7 20.8 + - - -
396A THR 4.2 2.0 - - - -
398A MET* 1.3 69.1 - - - +
400A SER* 1.3 61.2 + - - +
401A LEU 3.0 6.8 + - - -
402A TYR* 3.3 23.6 + - - -
403A TRP* 4.0 0.9 - - - -
425A VAL* 5.3 2.2 - - - -
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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