Contacts of the helix formed by residues 350 - 365 (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 ASN 350 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345H SER 5.0 0.8 + - - -
347H THR* 3.5 19.2 - - + +
348H THR* 3.1 13.8 + - - +
349H ASN* 1.3 72.8 - - - +
351H ILE* 1.3 69.5 + - + +
352H GLN 3.6 1.6 - - - -
353H SER* 3.4 8.5 + - - -
354H ARG* 2.8 60.9 + - - +
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Residues in contact with ILE 351 (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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301H VAL* 5.6 10.1 - - + -
305H ILE* 5.7 7.6 - - + -
340H ILE* 5.2 6.7 - - + -
341H CYS* 4.0 14.4 - - + -
344H PHE* 3.2 29.6 - - + +
345H SER* 4.3 5.6 - - - +
347H THR* 3.3 16.8 + - + +
350H ASN* 1.3 88.5 - - + +
352H GLN* 1.3 63.8 + - - +
354H ARG* 3.1 8.6 + - + +
355H ILE* 3.0 47.1 + - + +
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Residues in contact with GLN 352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341H CYS* 4.2 28.5 + - + +
342H LYS* 5.7 1.0 - - - +
345H SER* 3.9 27.8 + - - -
350H ASN 3.6 0.2 - - - -
351H ILE* 1.3 78.8 - - - +
353H SER* 1.3 52.8 + - - +
355H ILE* 3.9 4.8 - - - +
356H THR* 2.3 47.9 + - + +
383H LEU* 4.8 14.3 - - + +
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Residues in contact with SER 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349H ASN 4.8 7.9 - - - -
350H ASN* 3.4 11.8 + - - -
351H ILE 3.2 0.6 - - - -
352H GLN* 1.3 79.1 - - - +
354H ARG* 1.3 62.6 + - - +
356H THR* 3.0 5.9 + - - -
357H LYS* 2.9 48.5 + - - +
299I LYS* 6.4 1.3 - - - -
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Residues in contact with ARG 354 (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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305H ILE* 6.4 1.6 - - + -
350H ASN* 2.8 46.2 + - - +
351H ILE* 3.1 14.3 + - + +
353H SER* 1.3 78.6 - - - +
355H ILE* 1.3 62.5 + - + +
357H LYS* 3.3 12.9 + - - +
358H THR* 2.7 37.3 + - - +
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Residues in contact with ILE 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305H ILE* 4.7 19.3 - - + -
309H MET* 3.8 30.5 - - + -
337H VAL* 4.5 13.0 - - + -
341H CYS* 3.6 29.4 - - - -
351H ILE* 3.0 27.4 + - + +
352H GLN* 4.1 3.1 - - - +
354H ARG* 1.3 81.6 - - + +
356H THR* 1.3 59.7 + - + +
358H THR* 3.2 7.5 + - - -
359H PHE* 2.9 47.1 + - + -
383H LEU* 5.1 4.7 - - + -
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Residues in contact with THR 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352H GLN* 2.3 38.7 + - + +
353H SER* 3.0 13.7 + - - -
355H ILE* 1.3 74.4 - - + +
357H LYS* 1.3 53.6 + - - +
359H PHE* 3.4 6.1 + - - +
360H THR* 2.4 39.7 + - - -
380H LEU* 4.7 9.0 - - + +
383H LEU* 3.8 28.5 - - + -
387H VAL* 5.3 6.5 - - + -
391H LEU* 5.5 7.9 - - + -
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Residues in contact with LYS 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353H SER* 2.9 38.4 + - - +
354H ARG* 3.7 11.0 - - - +
356H THR* 1.3 76.3 + - - +
358H THR* 1.3 58.8 + - - +
360H THR* 3.2 8.9 + - - -
361H LYS* 3.0 44.7 + - - +
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Residues in contact with THR 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H MET* 3.8 23.1 - - + +
354H ARG* 2.7 27.9 + - - +
355H ILE* 3.3 9.0 - - - -
356H THR 3.2 0.2 - - - -
357H LYS* 1.3 78.2 - - - +
359H PHE* 1.3 53.6 + - + +
361H LYS* 3.4 6.0 + - - +
362H SER* 2.6 40.3 + - - +
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Residues in contact with PHE 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H MET* 3.6 27.6 - - + -
312H ILE* 5.1 15.7 - - + -
337H VAL* 5.0 6.7 - - + -
355H ILE* 2.9 32.9 + - + +
356H THR 3.8 1.8 - - - +
358H THR* 1.3 78.7 - - + +
360H THR* 1.3 56.7 + - - +
362H SER* 3.3 7.8 - - - -
363H TRP* 2.8 32.1 + - - +
375H GLY 4.6 2.5 - - - -
376H SER* 4.0 23.7 - - - +
379H GLY* 3.5 33.4 - - - -
380H LEU* 3.6 42.6 - - + +
383H LEU* 4.4 6.5 - - + -
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Residues in contact with THR 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356H THR* 2.4 27.2 + - - -
357H LYS* 3.4 9.8 - - - -
358H THR 3.1 0.4 - - - -
359H PHE* 1.3 74.6 - - - +
361H LYS* 1.3 63.3 + - + +
363H TRP* 3.0 5.8 + - + -
364H VAL* 3.0 48.3 + - + +
380H LEU* 5.3 2.6 - - - +
391H LEU* 5.6 8.0 - - + +
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Residues in contact with LYS 361 (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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357H LYS* 3.0 29.0 + - - +
358H THR* 3.9 4.9 - - - +
360H THR* 1.3 78.2 - - + +
362H SER* 1.3 62.2 + - - +
364H VAL* 5.1 2.5 - - - -
365H ASP* 3.8 26.3 + - - +
368H THR* 5.1 1.4 - - - +
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Residues in contact with SER 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358H THR* 2.6 27.7 + - - +
359H PHE* 3.3 11.8 - - - -
361H LYS* 1.3 79.7 - - - +
363H TRP* 1.3 62.2 + - - +
364H VAL 3.5 0.2 + - - -
365H ASP 4.0 0.3 + - - -
368H THR* 3.7 25.2 - - - +
372H THR* 4.9 8.9 + - - -
373H ARG* 4.7 5.2 - - - +
376H SER* 3.8 21.9 - - - -
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Residues in contact with TRP 363 (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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359H PHE 2.8 20.4 + - - +
360H THR* 3.0 5.8 + - + +
362H SER* 1.3 76.1 - - - +
364H VAL* 1.3 76.6 + - + +
365H ASP 4.2 0.2 - - - +
373H ARG* 4.9 7.4 + - + -
376H SER* 4.2 9.4 - - - +
377H ILE* 3.4 34.1 - - + +
380H LEU* 4.7 9.4 - - + -
391H LEU 3.2 20.0 - - - -
392H ILE* 3.5 47.3 - - + +
394H PRO* 4.6 2.7 - - + -
395H ARG* 3.5 38.6 - - + -
396H LEU* 4.1 2.0 - - - -
399H GLU* 2.7 58.5 + - - +
402H ARG* 4.1 5.9 + - - -
427H LEU* 5.8 2.0 - - + +
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Residues in contact with VAL 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360H THR* 3.0 32.5 + - + +
361H LYS* 4.9 1.8 - - - +
363H TRP* 1.3 93.3 - - + +
365H ASP* 1.3 69.8 + - - +
395H ARG* 3.4 37.6 + - - +
399H GLU* 4.7 2.7 - - - +
402H ARG* 2.7 28.1 + - - -
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Residues in contact with ASP 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361H LYS* 3.8 18.1 + - - +
362H SER 4.0 2.8 + - - -
363H TRP 3.5 2.0 - - - +
364H VAL* 1.3 92.3 - - - +
366H GLU* 1.3 66.9 + - - +
368H THR* 2.8 29.9 + - + +
402H ARG* 3.0 15.0 + - - +
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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