Contacts of the helix formed by residues 390 - 409 (chain A) in PDB entry 3CMQ
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 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A VAL* 4.8 0.7 - - - -
388A THR* 3.9 2.0 + - - -
389A LEU* 1.3 74.1 - - - +
391A GLN* 1.3 64.2 + - - +
392A ARG* 3.6 10.0 + - - +
393A GLU* 3.0 36.9 + - - +
394A VAL* 3.2 25.2 + - - +
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Residues in contact with GLN 391 (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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326A ALA 5.2 1.6 + - - -
327A VAL* 3.6 36.2 - - - +
389A LEU 4.0 1.8 + - - -
390A SER* 1.3 73.3 - - - +
392A ARG* 1.3 56.8 + - - +
394A VAL* 3.4 5.9 + - - +
395A ARG* 2.9 44.4 + - - +
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 3.7 9.6 - - - +
391A GLN* 1.3 76.7 - - - +
393A GLU* 1.3 66.8 + - + +
395A ARG* 3.0 45.1 + - - +
396A HIS* 3.2 45.2 + - + +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 4.9 6.9 - - + +
387A ARG* 2.8 45.5 + - - -
388A THR 4.1 0.2 - - - +
389A LEU* 3.5 13.0 - - + +
390A SER* 3.0 37.5 + - - +
392A ARG* 1.3 80.5 - - - +
394A VAL* 1.3 63.2 + - + +
396A HIS* 3.6 8.3 + - - +
397A ILE* 3.1 32.8 + - + +
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Residues in contact with VAL 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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327A VAL* 3.5 30.5 - - + -
329A ASN* 3.3 26.2 - - - +
356A LEU* 5.6 2.0 - - + -
382A TYR* 3.5 22.6 - - + -
389A LEU* 3.9 27.1 - - + -
390A SER 3.2 18.1 + - - +
391A GLN 3.6 4.0 - - - +
392A ARG 3.1 1.0 - - - -
393A GLU* 1.3 77.0 - - + +
395A ARG* 1.3 59.9 + - - +
397A ILE* 3.3 6.2 + - - +
398A HIS* 2.8 28.9 + - - +
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Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASN* 5.2 2.7 - - - +
391A GLN* 2.9 27.7 + - - +
392A ARG* 3.0 45.4 + - - +
394A VAL* 1.3 77.4 - - - +
396A HIS* 1.3 62.4 + - - +
398A HIS* 3.3 6.0 + - - +
399A GLN* 2.8 56.4 + - + +
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Residues in contact with HIS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ARG* 3.2 63.3 + - + +
393A GLU* 4.0 7.7 - - - +
395A ARG* 1.3 84.0 + - + +
397A ILE* 1.3 68.5 + - + +
399A GLN* 3.4 20.3 + - - +
400A ALA* 3.1 23.2 + - - +
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Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 3.8 18.7 - - + +
353A GLY* 4.0 25.4 - - - -
356A LEU* 4.0 22.2 - - + -
382A TYR* 4.0 18.4 - - + +
393A GLU* 3.1 21.7 + - + +
394A VAL* 3.7 5.4 - - - +
396A HIS* 1.3 77.7 - - + +
398A HIS* 1.3 62.9 + - - +
400A ALA* 3.3 7.8 + - + +
401A LEU* 3.1 21.2 + - + +
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Residues in contact with HIS 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASN* 3.4 40.1 - - + +
330A ASP 3.1 25.0 + - - -
331A ILE* 4.1 11.3 - - + +
380A ILE* 4.0 16.3 - - + +
382A TYR* 2.7 29.0 + + - +
394A VAL 2.8 17.8 + - - +
395A ARG* 3.6 5.6 - - - +
397A ILE* 1.3 75.9 - - - +
399A GLN* 1.3 65.4 + - + +
401A LEU* 3.1 8.6 + - + +
402A GLN* 3.0 42.8 + - - +
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Residues in contact with GLN 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ARG* 2.8 42.3 + - + +
396A HIS* 3.9 21.6 - - - +
398A HIS* 1.3 77.0 - - + +
400A ALA* 1.3 62.2 + - - +
402A GLN* 3.2 20.5 + - - +
403A GLU* 3.1 37.8 + - - +
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 4.1 17.6 - - + +
396A HIS 3.1 18.4 + - - +
397A ILE* 3.6 8.7 - - + +
398A HIS 3.2 0.2 - - - -
399A GLN* 1.3 76.7 - - - +
401A LEU* 1.3 58.1 + - - +
403A GLU* 4.0 10.7 - - - +
404A ALA* 3.0 30.7 + - - +
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 4.1 12.6 - - + -
345A PHE* 3.9 14.4 - - + -
348A LEU* 4.1 20.6 - - + +
349A VAL* 3.9 33.0 - - + -
352A ILE* 4.3 11.2 - - + -
380A ILE* 3.3 34.5 - - + -
382A TYR* 4.2 9.4 - - - +
397A ILE* 3.1 14.5 + - + +
398A HIS* 3.1 10.7 + - - +
400A ALA* 1.3 75.1 - - - +
402A GLN* 1.3 59.7 + - - +
404A ALA* 3.4 3.2 + - - +
405A ALA* 2.8 31.7 + - - +
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Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASP 5.0 2.6 + - - -
331A ILE* 3.9 20.3 - - + +
398A HIS* 3.0 35.1 + - + +
399A GLN* 3.5 28.5 + - - +
401A LEU* 1.3 76.2 - - - +
403A GLU* 1.3 63.6 + - + +
405A ALA* 3.3 4.5 + - - +
406A VAL* 3.2 27.8 + - - +
415A PHE* 3.0 55.1 - - + +
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLN* 3.1 23.3 + - - +
400A ALA* 4.0 8.8 - - - +
402A GLN* 1.3 77.0 - - + +
404A ALA* 1.3 63.0 + - - +
406A VAL* 3.2 9.4 + - - +
407A GLN* 3.0 27.7 + - + +
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Residues in contact with ALA 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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348A LEU* 3.8 23.6 - - + -
352A ILE* 4.3 13.5 - - + -
400A ALA 3.0 19.7 + - - +
401A LEU* 3.7 3.8 - - - +
402A GLN 3.3 0.2 - - - -
403A GLU* 1.3 73.7 - - - +
405A ALA* 1.3 61.4 + - - +
407A GLN* 3.0 6.5 + - - -
408A LEU* 2.8 40.2 + - + +
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Residues in contact with ALA 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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331A ILE* 4.7 0.4 - - + -
333A PHE* 4.3 17.7 - - + -
345A PHE* 4.6 4.7 - - + -
348A LEU* 3.5 16.9 - - + +
401A LEU 2.8 19.0 + - - +
402A GLN* 3.3 8.5 + - - +
404A ALA* 1.3 75.5 - - - +
406A VAL* 1.3 58.9 + - - +
409A LEU* 3.1 35.8 + - + +
410A GLY 3.3 1.6 + - - -
411A VAL* 3.1 20.2 - - + +
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Residues in contact with VAL 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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333A PHE* 6.0 0.2 - - + -
402A GLN 3.2 15.8 + - - +
403A GLU* 3.6 9.4 - - - +
404A ALA 3.1 0.4 - - - -
405A ALA* 1.3 78.8 - - - +
407A GLN* 1.3 68.7 + - - +
410A GLY* 3.8 14.2 + - - -
411A VAL* 3.5 26.6 - - + +
412A GLU* 5.4 0.2 - - - -
413A GLY* 3.9 22.7 - - - +
415A PHE* 4.8 5.8 - - + -
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Residues in contact with GLN 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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403A GLU* 3.0 21.3 + - + +
404A ALA* 3.0 8.1 + - - +
406A VAL* 1.3 88.1 + - - +
408A LEU* 1.3 74.1 + - + +
410A GLY* 4.5 2.5 + - - -
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Residues in contact with LEU 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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11A PRO* 6.5 1.3 - - + -
348A LEU* 3.7 25.1 - - + -
404A ALA* 2.8 23.4 + - + +
407A GLN* 1.3 87.2 - - + +
409A LEU* 1.3 70.0 + - + +
410A GLY 3.2 1.9 + - - -
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Residues in contact with LEU 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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333A PHE* 4.8 0.2 - - + -
336A PRO* 2.8 23.9 - - - +
339A ASN 4.3 2.1 - - - +
340A TYR* 3.9 17.1 - - + -
344A ASP* 4.7 11.4 - - + +
345A PHE* 3.5 50.3 - - + +
348A LEU* 3.3 34.3 - - + -
405A ALA* 3.1 16.8 + - + +
408A LEU* 1.3 84.3 - - + +
410A GLY* 1.3 57.5 + - - +
411A VAL* 3.7 10.3 - - + -
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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
------------------------------------------------------------
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