Contacts of the helix formed by residues 380 - 392 (chain H) in PDB entry 6NZD
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 380 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344H PRO* 4.4 12.8 - - - +
378H SER* 2.8 13.7 + - - +
379H ARG* 1.3 78.0 - - + +
381H VAL* 1.3 66.2 + - - +
382H ASP* 3.3 8.9 + - - +
383H LEU* 3.1 27.6 + - + +
384H VAL* 3.2 23.7 + - - +
463H TYR* 2.7 35.7 + - + +
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Residues in contact with VAL 381 (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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379H ARG 3.6 3.5 + - - +
380H ASP* 1.3 70.1 + - - +
382H ASP* 1.3 72.0 + - - +
384H VAL* 3.3 4.2 + - - +
385H GLN* 3.1 24.2 + - + +
405H TYR* 3.3 56.9 - - + +
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Residues in contact with ASP 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345H VAL* 3.9 13.2 - - + +
380H ASP* 3.3 7.0 + - - +
381H VAL* 1.3 80.8 - - - +
383H LEU* 1.3 66.1 + - - +
385H GLN* 3.4 8.9 + - - +
386H SER* 3.0 23.0 + - - -
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Residues in contact with LEU 383 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344H PRO 3.6 20.8 + - - +
345H VAL* 4.2 1.1 - - - +
346H PHE* 3.7 25.1 - - + -
376H TRP* 5.4 1.8 - - + -
378H SER* 4.3 9.2 - - - +
380H ASP* 3.1 27.5 + - - +
381H VAL 3.2 0.2 - - - -
382H ASP* 1.3 76.4 - - - +
384H VAL* 1.3 63.2 + - + +
386H SER* 2.6 23.7 + - - +
387H ALA* 3.2 7.8 + - - +
441H VAL* 4.1 23.6 - - + -
460H LEU* 3.9 15.9 - - + -
463H TYR* 4.0 24.2 - - + -
465H PHE* 4.3 9.2 - - + -
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Residues in contact with VAL 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376H TRP* 4.2 20.9 - - + +
378H SER* 3.6 29.6 - - - +
380H ASP 3.2 14.9 + - - +
381H VAL 3.7 7.4 - - - +
382H ASP 3.3 0.2 - - - -
383H LEU* 1.3 76.0 - - + +
385H GLN* 1.3 64.9 + - - +
387H ALA* 3.1 17.1 + - - +
388H PHE* 3.3 36.8 + - + -
404H PRO 3.7 16.4 - - - +
405H TYR* 4.5 10.1 - - + -
419H GLY* 3.9 9.9 - - - -
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Residues in contact with GLN 385 (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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381H VAL* 3.1 17.2 + - + +
382H ASP* 3.7 11.9 - - - +
383H LEU 3.3 0.2 - - - -
384H VAL* 1.3 76.4 - - - +
386H SER* 1.3 64.1 + - - +
387H ALA 3.2 0.3 + - - -
388H PHE* 3.3 7.2 + - - +
389H GLU* 3.0 47.2 + - - +
392H ARG* 5.1 6.4 + - - -
402H ILE* 4.7 10.4 - - - +
404H PRO* 3.5 31.7 + - - +
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Residues in contact with SER 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345H VAL* 3.5 29.4 - - - +
346H PHE* 3.0 29.4 + - - -
382H ASP 3.0 9.7 + - - -
383H LEU 2.6 19.6 + - - -
385H GLN* 1.3 76.8 - - - +
387H ALA* 1.3 61.2 + - - +
389H GLU* 3.4 17.3 + - - +
390H VAL* 3.0 27.2 + - - +
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Residues in contact with ALA 387 (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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346H PHE* 4.0 5.6 - - + -
352H MET* 3.7 9.7 - - + +
376H TRP* 3.8 47.8 - - + +
383H LEU 3.2 6.9 + - - +
384H VAL 3.1 9.9 + - - +
386H SER* 1.3 81.3 + - - +
388H PHE* 1.3 57.8 + - + +
390H VAL* 3.3 2.4 + - - -
391H LEU* 2.9 34.9 + - - +
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Residues in contact with PHE 388 (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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374H VAL* 3.9 11.7 - - + -
376H TRP* 3.8 26.7 - + + -
384H VAL* 3.3 35.4 + - + -
385H GLN* 3.3 11.3 + - - +
387H ALA* 1.3 75.4 - - - +
389H GLU* 1.3 62.4 + - - +
391H LEU* 4.4 8.1 - - + +
392H ARG* 3.0 32.9 + - - +
402H ILE* 3.8 30.3 - - + -
404H PRO* 4.3 5.2 - - + -
417H PHE* 3.8 30.4 - + + -
418H LEU 3.4 27.4 - - - -
419H GLY* 3.6 13.2 - - - -
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Residues in contact with GLU 389 (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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385H GLN* 3.0 40.4 + - + +
386H SER* 3.5 18.3 - - - +
388H PHE* 1.3 74.4 - - - +
390H VAL* 1.3 65.3 + - + +
392H ARG* 3.3 26.1 - - - +
393H THR* 3.7 9.0 - - - +
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Residues in contact with VAL 390 (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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346H PHE* 4.2 13.0 - - + +
347H LYS 4.2 2.0 - - - +
348H SER* 3.6 29.4 - - - +
349H LEU* 3.4 40.6 - - + +
352H MET* 4.1 15.7 - - + -
386H SER 3.0 19.3 + - - +
387H ALA 3.8 3.1 - - - +
388H PHE 3.3 0.2 - - - -
389H GLU* 1.3 76.7 - - + +
391H LEU* 1.3 61.9 + - - +
393H THR* 2.8 30.8 + - - +
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Residues in contact with LEU 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349H LEU* 4.8 2.9 - - + -
352H MET* 3.6 24.5 - - + -
361H PHE* 5.0 1.8 - - + -
364H LEU* 4.0 16.8 - - + -
368H VAL* 4.1 19.2 - - + +
374H VAL* 4.2 17.0 - - + -
376H TRP* 3.6 29.2 - - + +
387H ALA 2.9 23.1 + - - +
388H PHE* 4.3 8.7 - - + +
389H GLU 3.4 0.2 - - - -
390H VAL* 1.3 76.7 - - - +
392H ARG* 1.3 62.8 + - - +
393H THR 3.1 1.4 + - - -
394H MET* 3.1 44.2 + - + +
417H PHE* 4.4 9.4 - - + -
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Residues in contact with ARG 392 (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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385H GLN* 5.1 7.3 + - - -
388H PHE 3.0 22.0 + - - +
389H GLU* 3.3 23.0 - - - +
391H LEU* 1.3 71.7 - - - +
393H THR* 1.3 65.1 + - + +
394H MET 2.9 6.9 + - - -
395H LEU* 3.1 23.8 + - - +
397H VAL* 5.2 11.1 - - - +
400H VAL* 4.3 34.4 - - + +
402H ILE* 4.8 19.4 - - - +
417H PHE* 4.2 18.3 - - + -
508H LYS* 4.1 0.5 + - - -
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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