Contacts of the helix formed by residues 392 - 409 (chain A) in PDB entry 3JRQ
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 ASP 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.8 33.0 - - + +
129A TYR 2.7 30.6 + - - +
369A TRP* 6.2 0.3 - - - -
390A GLY 3.8 1.4 + - - +
391A LYS* 1.3 70.3 - - - +
393A PRO* 1.3 78.6 - - - +
394A ALA* 3.6 13.2 + - - +
395A ALA* 3.1 23.3 + - + +
396A MET* 2.8 25.3 + - - +
421A ASP* 4.5 6.2 - - - +
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Residues in contact with PRO 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A TRP* 3.6 40.3 - - + +
391A LYS 3.8 7.4 - - - +
392A ASP* 1.3 90.7 - - - +
394A ALA* 1.3 52.4 + - - +
396A MET* 2.8 11.5 + - + +
397A SER* 2.7 35.8 + - - -
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ARG 4.7 0.2 - - - -
366A ILE* 3.6 38.0 + - + +
369A TRP* 3.9 37.9 - - + -
392A ASP* 3.3 13.1 + - - +
393A PRO* 1.3 79.9 - - - +
395A ALA* 1.3 58.0 + - - +
397A SER* 3.5 4.3 - - - -
398A ALA* 3.1 21.5 + - - +
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU 4.6 2.0 - - - +
129A TYR* 3.5 10.5 - - - +
130A GLY* 3.4 22.7 - - - +
366A ILE* 4.2 9.3 - - + +
392A ASP* 3.1 19.1 + - - +
394A ALA* 1.3 73.8 - - - +
396A MET* 1.3 65.6 + - - +
397A SER 3.2 0.2 - - - -
398A ALA* 3.3 0.6 + - - -
399A ALA* 3.0 6.9 + - - +
419A VAL* 2.9 41.8 - - + +
421A ASP 4.8 4.0 - - - +
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Residues in contact with MET 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR 4.6 0.7 - - - +
130A GLY* 3.5 4.5 - - - -
131A PHE* 3.4 49.8 - - + +
391A LYS* 3.5 36.8 - - + -
392A ASP 2.8 22.5 + - - +
393A PRO* 2.8 12.5 + - + +
395A ALA* 1.3 72.2 - - - +
397A SER* 1.3 57.0 - - - +
399A ALA* 3.4 2.9 + - - +
400A GLU* 3.0 36.5 + - + +
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ARG* 4.6 3.7 + - - +
369A TRP* 4.4 21.5 - - - +
393A PRO 2.7 14.8 + - - -
394A ALA* 3.5 10.5 - - - -
396A MET* 1.3 73.1 - - - +
398A ALA* 1.3 56.1 + - - +
400A GLU* 3.1 8.8 + - - +
401A TYR* 2.9 56.0 + - - -
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A MET* 5.4 0.2 - - - +
362A ALA* 3.6 38.3 - - + +
365A ARG* 4.2 12.7 - - + +
366A ILE* 4.0 8.1 - - + -
394A ALA 3.1 16.2 + - - +
395A ALA 3.3 4.0 + - - +
397A SER* 1.3 72.3 + - - +
399A ALA* 1.3 65.3 + - - +
401A TYR* 3.5 2.8 + - - +
402A LEU* 3.1 30.4 + - - +
419A VAL* 4.2 8.7 - - + -
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Residues in contact with ALA 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 3.8 23.3 - - - +
132A THR* 3.4 21.2 + - - +
395A ALA 3.0 7.1 + - - +
396A MET 3.6 8.5 - - - +
398A ALA* 1.3 75.7 - - - +
400A GLU* 1.3 62.2 + - - +
402A LEU* 3.5 2.3 + - - +
403A SER* 3.2 18.2 + - - -
417A VAL* 4.1 18.7 - - + +
419A VAL* 3.4 22.9 - - + +
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Residues in contact with GLU 400 (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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131A PHE 5.6 2.0 - - - +
132A THR* 3.1 32.6 + - + +
134A ILE* 5.3 0.7 - - - +
396A MET* 3.0 20.1 + - + +
397A SER* 3.1 12.1 + - - +
399A ALA* 1.3 74.4 - - - +
401A TYR* 1.3 65.4 + - + +
402A LEU 3.1 1.3 - - - -
403A SER* 3.0 12.6 + - - -
404A LYS* 3.0 45.4 + - + +
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Residues in contact with TYR 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A MET* 4.3 15.2 - - + +
365A ARG* 3.3 54.6 + - + -
397A SER* 2.9 49.9 + - - +
398A ALA 3.9 3.4 - - - +
400A GLU* 1.3 73.6 - - + +
402A LEU* 1.3 59.0 + - - +
404A LYS* 3.8 17.2 - - + +
405A LEU* 2.9 32.4 + - - +
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE* 4.3 18.8 - - + -
349A VAL* 4.6 5.9 - - + +
353A MET* 3.5 26.8 - - + +
358A ALA* 3.8 25.1 - - + +
361A MET* 3.7 25.1 - - + -
362A ALA* 4.2 17.5 - - + -
398A ALA 3.1 21.0 + - - +
399A ALA 3.6 5.2 - - - +
401A TYR* 1.3 79.9 - - - +
403A SER* 1.3 61.4 + - - +
405A LEU* 3.6 2.2 + - + -
406A ALA* 3.1 21.5 + - - +
417A VAL* 3.9 27.4 - - + -
419A VAL* 5.5 1.6 - - + -
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Residues in contact with SER 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 3.8 9.5 + - - -
134A ILE* 3.9 17.5 - - - +
399A ALA 3.2 9.3 + - - -
400A GLU* 3.0 30.0 + - - -
402A LEU* 1.3 76.9 - - - +
404A LYS* 1.3 61.3 + - - +
406A ALA* 3.2 2.6 + - - +
407A ILE* 2.8 33.0 + - - +
415A ILE* 3.4 31.2 - - - +
417A VAL* 4.9 3.7 - - - +
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Residues in contact with LYS 404 (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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134A ILE* 6.2 0.9 - - + -
400A GLU* 3.0 43.6 + - + +
401A TYR* 3.9 16.4 - - + +
403A SER* 1.3 76.5 - - - +
405A LEU* 1.3 54.6 + - - +
407A ILE* 3.3 12.5 + - + +
408A GLN* 2.7 46.7 + - - +
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Residues in contact with LEU 405 (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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353A MET* 3.4 37.0 - - + -
357A GLU* 5.4 4.0 - - + +
361A MET* 4.2 26.2 - - + -
401A TYR 2.9 16.6 + - - +
402A LEU* 3.8 6.7 - - + +
404A LYS* 1.3 75.2 - - - +
406A ALA* 1.3 58.1 + - - +
408A GLN* 3.2 21.2 + - + +
409A ARG* 2.9 70.0 + - + +
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Residues in contact with ALA 406 (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 GLY 3.8 15.9 - - - +
349A VAL* 4.6 1.8 - - - -
352A VAL* 3.8 12.9 - - + +
353A MET* 4.2 9.4 - - + -
402A LEU 3.1 14.4 + - - +
403A SER* 3.4 10.8 - - - +
405A LEU* 1.3 74.2 - - - +
407A ILE* 1.3 64.0 + - - +
409A ARG* 3.2 7.8 + - - -
411A SER* 3.0 26.7 + - - -
415A ILE* 3.7 19.3 - - + -
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Residues in contact with ILE 407 (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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134A ILE* 3.7 16.2 - - + -
136A GLY* 3.5 24.7 - - - -
137A ARG 4.9 0.4 - - - +
403A SER 2.8 16.0 + - - +
404A LYS* 3.3 14.8 - - + +
406A ALA* 1.3 72.3 - - - +
408A GLN* 1.3 61.4 + - + +
410A GLY* 2.7 25.8 + - - -
411A SER 4.8 4.0 - - - +
415A ILE* 3.4 24.0 - - + -
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Residues in contact with GLN 408 (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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404A LYS* 2.7 31.0 + - - +
405A LEU* 3.2 23.7 + - + +
407A ILE* 1.3 76.5 - - + +
409A ARG* 1.3 61.3 + - + +
410A GLY 3.4 2.4 + - - -
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Residues in contact with ARG 409 (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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352A VAL* 3.0 54.9 + - + +
353A MET* 3.6 7.8 - - - +
357A GLU* 3.3 35.0 + - - -
405A LEU* 2.9 41.3 + - + +
406A ALA 3.2 0.4 + - - -
407A ILE 3.1 0.6 - - - -
408A GLN* 1.3 81.6 - - + +
410A GLY* 1.3 59.1 + - - +
411A SER 3.4 3.3 + - - -
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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