Contacts of the helix formed by residues 387 - 399 (chain A) in PDB entry 3QPV
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 HIS 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ARG* 4.1 6.3 - - - -
253A HIS* 3.5 7.5 - + - -
256A ASN* 6.2 0.2 - - - -
298A SER* 2.9 22.6 + - - -
300A LEU* 3.5 28.8 - - + +
302A SER* 4.3 4.7 - - - -
303A THR* 3.3 15.2 - - + +
320A LEU 3.4 23.3 - - - -
322A GLU* 3.5 33.3 - - + +
386A CYS* 1.3 83.8 - - - +
388A GLN* 1.3 68.1 + - - +
389A ALA 3.5 0.4 - - - -
390A VAL* 3.3 2.5 + - + +
391A LEU* 2.7 22.2 + - - +
710A PHS 2.8 28.2 + - - +
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Residues in contact with GLN 388 (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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252A ARG* 3.0 26.8 + - - +
322A GLU* 3.4 1.4 + - - -
333A TYR* 4.9 1.0 + - - -
387A HIS* 1.3 74.5 - - - +
389A ALA* 1.3 62.4 + - - +
391A LEU* 3.3 2.8 + - - +
392A ARG* 3.0 60.5 + - + +
411A CYS* 4.0 9.7 - - + +
440A THR* 2.8 44.6 + - - +
441A HIS* 3.9 4.3 + - - +
710A PHS 2.7 9.0 + - - -
720A F6P 3.0 44.5 + - - +
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Residues in contact with ALA 389 (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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322A GLU* 2.9 25.1 + - - +
323A ILE* 3.7 17.5 - - + -
362A TYR* 3.5 29.6 - - + +
365A LEU* 3.7 13.9 - - + -
388A GLN* 1.3 70.7 - - - +
390A VAL* 1.3 65.7 + - - +
392A ARG* 3.3 4.6 + - - +
393A CYS* 3.0 26.5 + - - -
720A F6P 4.3 2.7 - - - -
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Residues in contact with VAL 390 (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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320A LEU* 3.6 28.7 - - + +
321A ASN 3.4 25.1 - - - +
322A GLU* 3.2 12.3 + - - +
365A LEU* 3.8 21.8 - - + -
368A ARG* 4.7 0.9 - - - +
369A LEU* 4.0 13.9 - - + +
386A CYS* 3.8 25.6 - - + -
387A HIS 3.6 9.2 - - - +
388A GLN 3.3 0.2 - - - -
389A ALA* 1.3 77.5 - - - +
391A LEU* 1.3 64.2 + - - +
393A CYS* 2.9 13.9 + - - +
394A LEU* 3.0 16.3 + - + +
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Residues in contact with LEU 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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250A LEU* 3.6 35.0 - - + +
251A CYS* 3.4 43.1 - - - +
252A ARG* 3.7 14.1 - - + -
386A CYS* 3.9 11.2 - - - -
387A HIS 2.7 22.0 + - - +
388A GLN* 3.6 4.0 - - - +
390A VAL* 1.3 69.4 - - - +
392A ARG* 1.3 67.0 + - - +
394A LEU* 3.1 4.3 + - + +
395A LEU* 2.8 23.1 + - + +
411A CYS* 4.1 18.6 - - + -
412A PRO 5.9 0.9 - - - +
415A THR 5.5 1.1 - - - +
417A LEU* 4.4 14.8 - - + -
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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
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351A LYS* 4.6 1.0 - - - +
362A TYR* 3.0 24.1 + - + -
388A GLN* 3.0 39.4 + - - +
389A ALA 3.4 6.1 - - - +
391A LEU* 1.3 74.1 - - - +
393A CYS* 1.3 54.3 + - - +
395A LEU* 4.4 0.2 - - - -
396A ALA* 2.8 36.7 + - - +
406A MET* 3.3 28.3 - - - +
407A PRO 3.2 16.7 + - - -
408A TYR* 4.9 0.2 - - - +
409A LEU* 2.7 23.8 + - + +
411A CYS* 3.7 20.0 - - - -
441A HIS* 3.3 35.1 + - - +
442A ARG 4.6 3.6 + - - +
720A F6P 2.6 35.0 + - - -
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Residues in contact with CYS 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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60A TRP* 2.8 30.3 + - + +
362A TYR* 3.6 22.0 - - - -
365A LEU* 3.4 29.4 - - + -
366A VAL* 4.7 4.7 - - + -
369A LEU* 3.6 15.9 - - + -
389A ALA 3.0 17.8 + - - -
390A VAL 2.9 9.5 + - - +
392A ARG* 1.3 77.7 - - - +
394A LEU* 1.3 62.7 + - - +
396A ALA* 3.7 1.2 + - - +
397A TYR 3.3 5.4 + - - -
406A MET* 3.7 18.4 - - - -
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Residues in contact with LEU 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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60A TRP* 5.0 0.7 - - + +
250A LEU* 4.2 20.2 - - + -
320A LEU* 4.1 22.0 - - + -
369A LEU* 4.3 17.7 - - + -
372A VAL* 4.3 15.7 - - + -
373A ILE* 3.4 29.2 - - + -
376A LEU* 4.7 4.3 - - + -
384A VAL* 4.2 16.2 - - + -
386A CYS* 4.4 6.5 - - - -
390A VAL* 3.0 22.4 + - + +
391A LEU* 3.7 5.2 - - - +
393A CYS* 1.3 74.3 - - - +
395A LEU* 1.4 66.9 + - - +
397A TYR* 2.9 14.3 + - - +
398A PHE* 3.0 24.4 + - + -
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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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250A LEU* 4.1 15.7 - - + +
391A LEU* 2.8 24.8 + - + +
392A ARG 3.6 3.1 - - - +
394A LEU* 1.4 69.4 - - - +
396A ALA* 1.3 57.4 + - - +
398A PHE* 2.9 3.9 + - - +
399A LEU* 2.7 65.0 + - + +
409A LEU* 4.1 21.5 - - + -
410A LYS 4.7 4.5 - - - +
411A CYS* 4.3 9.9 - - - -
417A LEU* 3.7 33.2 - - + -
419A LEU* 4.3 16.6 - - + -
428A VAL* 4.8 1.6 - - + -
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Residues in contact with ALA 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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60A TRP* 4.1 2.8 - - - +
392A ARG 2.8 20.3 + - - +
393A CYS 3.8 1.3 - - - +
395A LEU* 1.3 70.7 - - - +
397A TYR* 1.3 63.2 + - - +
400A ASP* 3.0 5.5 + - - -
401A LYS* 2.9 48.4 + - + +
406A MET* 3.3 43.5 - - + -
409A LEU* 3.8 3.4 - - + +
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Residues in contact with TYR 397 (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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56A ARG* 3.0 46.5 + - - +
57A TYR* 3.8 27.8 - + + -
60A TRP* 3.4 49.8 - + + +
237A TYR* 2.8 22.3 + - - -
373A ILE* 3.5 36.8 - - + -
377A GLU* 2.5 32.8 + - - +
393A CYS 3.3 3.6 + - - +
394A LEU 2.9 10.2 + - - +
396A ALA* 1.3 83.3 - - - +
398A PHE* 1.3 81.6 + + - +
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Residues in contact with PHE 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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56A ARG* 3.8 18.6 + - - +
246A ARG* 5.7 0.4 - - - -
248A ILE* 3.6 33.9 - - + -
250A LEU* 4.5 4.3 - - + -
373A ILE* 4.1 5.6 - - + -
376A LEU* 3.9 31.9 - - + -
377A GLU* 4.3 9.2 - - - -
394A LEU* 3.0 32.3 + - + -
395A LEU* 2.9 6.4 + - - +
397A TYR* 1.3 104.0 - + - +
399A LEU* 1.3 68.6 + - + +
400A ASP 3.3 2.1 + - - -
419A LEU* 3.7 30.7 - - + -
425A GLY* 5.5 0.3 - - - -
426A CYS* 4.1 31.3 + - - +
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Residues in contact with LEU 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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395A LEU* 2.7 48.4 + - + +
398A PHE* 1.3 79.5 - - + +
400A ASP* 1.3 71.2 + - - +
401A LYS* 3.2 36.5 + - + +
419A LEU* 3.8 23.3 - - + -
426A CYS* 4.2 19.3 - - + +
428A VAL* 4.2 25.4 - - + -
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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