Contacts of the helix formed by residues 395 - 407 (chain H) in PDB entry 6MZL
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 ARG 395 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363H TRP* 3.5 26.5 - - + -
364H VAL* 3.4 40.6 + - - +
394H PRO* 1.3 86.8 - - + +
396H LEU* 1.3 58.1 + - - +
397H GLN 3.3 1.3 - - - +
398H GLN* 3.3 40.2 + - + +
399H GLU* 2.9 37.4 + - + +
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Residues in contact with LEU 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363H TRP* 3.7 4.0 - - - -
392H ILE* 3.1 23.1 + - + +
393H LEU* 3.3 29.2 - - + +
394H PRO 3.2 0.2 - - - -
395H ARG* 1.3 75.0 - - - +
397H GLN* 1.3 66.2 + - + +
399H GLU* 3.8 2.1 - - - +
400H GLY* 2.9 26.5 + - - -
427H LEU* 4.8 28.7 - - + +
431H CYS* 4.9 15.3 - - - -
435H LEU* 5.3 8.7 - - + -
451H GLU* 4.3 26.0 - - + +
455H LEU* 6.0 7.4 - - + -
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Residues in contact with GLN 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393H LEU 5.3 1.9 + - - +
394H PRO 4.1 8.3 + - - +
395H ARG 3.3 0.6 - - - -
396H LEU* 1.3 85.0 - - + +
398H GLN* 1.3 61.7 + - + +
400H GLY* 3.3 2.8 + - - -
401H GLU* 2.9 34.3 + - + +
449H ARG 5.1 0.8 + - - -
450H ALA 2.8 30.3 + - - -
451H GLU* 3.4 12.1 - - - +
452H PHE* 3.6 32.3 - - + +
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Residues in contact with GLN 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394H PRO 5.2 2.2 + - - +
395H ARG* 3.3 50.9 + - + +
396H LEU 3.3 0.6 - - - -
397H GLN* 1.3 80.3 - - + +
399H GLU* 1.3 60.0 + - + +
401H GLU* 3.1 16.2 + - - +
402H ARG* 2.9 29.2 + - - +
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Residues in contact with GLU 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H TRP* 2.7 74.7 + - - +
364H VAL* 4.7 1.9 - - - +
373H ARG* 3.3 25.3 + - - +
377H ILE* 4.3 6.9 - - - +
395H ARG* 2.9 18.2 + - + +
396H LEU* 4.1 2.7 - - - +
398H GLN* 1.3 75.3 - - + +
400H GLY* 1.3 60.3 - - - +
402H ARG* 3.1 20.5 + - - +
403H ILE* 2.9 36.3 + - + +
427H LEU* 5.8 6.3 - - + +
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Residues in contact with GLY 400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396H LEU 2.9 16.4 + - - -
397H GLN* 3.3 5.6 + - - -
399H GLU* 1.3 77.2 - - - +
401H GLU* 1.3 56.2 + - - +
403H ILE* 3.2 11.5 + - - +
404H ARG* 2.8 36.2 + - - +
427H LEU* 5.9 3.7 - - - +
452H PHE* 6.2 2.0 - - - -
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Residues in contact with GLU 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397H GLN* 2.9 19.8 + - - +
398H GLN* 3.1 15.8 + - - +
400H GLY* 1.3 72.8 - - - +
402H ARG* 1.3 62.1 + - - +
404H ARG* 3.5 26.8 + - + +
405H SER* 2.8 28.4 + - - -
452H PHE* 5.8 2.7 - - + +
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Residues in contact with ARG 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363H TRP 4.1 6.1 + - - -
364H VAL 2.7 27.6 + - - -
365H ASP 3.0 27.1 + - - -
366H GLU* 3.5 15.8 - - - +
368H THR* 3.8 2.6 + - - -
370H TRP* 5.2 0.7 - - + -
373H ARG* 3.2 50.2 - - - +
398H GLN* 2.9 18.6 + - - +
399H GLU* 3.1 18.7 + - - +
401H GLU* 1.3 74.9 - - - +
403H ILE* 1.3 57.1 + - - +
405H SER* 2.3 28.0 + - - -
406H VAL* 2.9 16.9 + - - +
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Residues in contact with ILE 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370H TRP* 4.1 11.0 - - + -
373H ARG* 5.1 3.1 - - - +
399H GLU* 2.9 18.9 + - + +
400H GLY* 3.6 9.9 - - - +
402H ARG* 1.3 74.0 - - + +
404H ARG* 1.3 55.0 + - - +
406H VAL* 3.0 7.8 + - + -
407H LEU* 2.4 39.1 + - + +
420H ALA* 3.7 29.4 - - + +
423H VAL* 3.7 29.2 - - + -
424H GLN* 3.4 34.5 - - + +
427H LEU* 4.5 11.7 - - + -
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Residues in contact with ARG 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400H GLY 2.8 20.9 + - - +
401H GLU* 3.2 27.0 + - + +
403H ILE* 1.3 76.7 - - - +
405H SER* 1.3 57.6 + - - +
407H LEU* 2.8 39.8 - - + +
408H ASP* 3.6 11.9 - - - +
452H PHE* 2.4 45.4 + - - +
453H GLY* 3.4 4.9 - - - -
454H SER* 3.1 28.5 - - - +
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Residues in contact with SER 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401H GLU 2.8 11.8 + - - -
402H ARG* 2.3 32.4 + - - -
404H ARG* 1.3 74.8 - - - +
406H VAL* 1.3 60.9 + - - +
407H LEU 2.9 11.7 - - - +
409H GLY* 4.5 1.0 + - - -
410H PRO* 4.4 12.5 - - - +
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Residues in contact with VAL 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370H TRP* 3.6 29.8 - - + +
402H ARG 2.9 18.9 + - - +
403H ILE* 3.0 10.7 + - + +
405H SER* 1.3 76.5 - - - +
407H LEU* 1.3 63.5 + - + +
409H GLY 4.5 0.3 + - - -
410H PRO* 4.3 7.8 - - - +
416H ASP* 4.1 16.4 - - + +
417H ARG* 3.8 32.2 + - + +
420H ALA* 4.0 18.4 - - + -
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Residues in contact with LEU 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403H ILE* 2.4 33.7 + - + +
404H ARG* 2.8 35.1 - - + +
405H SER* 2.9 11.4 - - - +
406H VAL* 1.3 70.6 - - + +
408H ASP* 1.3 71.0 + - - +
409H GLY 2.8 15.1 + - - -
417H ARG* 4.5 14.8 - - + +
424H GLN* 4.2 23.6 - - - +
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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