Contacts of the helix formed by residues 349 - 365 (chain I) 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 349 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345I SER* 2.8 30.6 - - - +
346I THR 4.5 0.5 - - - +
347I THR 2.8 12.5 + - - +
348I THR* 1.3 71.8 - - - +
350I ASN* 1.3 62.5 + - - +
351I ILE 3.1 3.1 - - - +
352I GLN* 4.3 6.0 - - + +
353I SER* 3.2 38.7 + - - +
354I ARG* 3.5 3.1 + - - +
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Residues in contact with ASN 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386H ASP* 5.9 2.0 - - - -
301I VAL* 6.0 0.2 - - - +
302I HIS* 3.7 31.4 + - + -
348I THR* 3.1 10.9 + - - +
349I ASN* 1.3 75.2 - - - +
351I ILE* 1.3 72.7 + - + +
354I ARG* 2.7 53.4 + - - +
355I ILE* 3.5 3.5 + - - +
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Residues in contact with ILE 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301I VAL* 5.2 13.7 - - + -
302I HIS* 5.9 2.0 - - + -
305I ILE* 5.7 5.4 - - + -
340I ILE* 4.8 8.7 - - + -
341I CYS* 3.7 43.2 - - + +
344I PHE* 3.7 43.7 - - + +
345I SER* 3.7 14.6 - - - +
348I THR 4.9 1.3 - - - +
349I ASN 3.1 0.2 - - - -
350I ASN* 1.3 91.5 - - + +
352I GLN* 1.3 65.3 + - + +
355I ILE* 3.0 35.8 + - + +
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Residues in contact with GLN 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341I CYS* 4.9 12.6 + - + +
345I SER* 3.5 31.0 + - - +
349I ASN* 4.0 5.6 + - + +
351I ILE* 1.3 82.7 - - + +
353I SER* 1.3 53.9 + - - +
355I ILE* 5.2 0.2 - - - -
356I THR* 2.3 49.0 + - + +
383I LEU* 5.8 6.3 - - + -
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Residues in contact with SER 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349I ASN* 3.2 26.4 + - - -
352I GLN* 1.3 77.9 - - - +
354I ARG* 1.3 61.6 + - - +
356I THR* 2.8 16.6 + - - -
357I LYS* 2.9 43.0 + - - +
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Residues in contact with ARG 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H HIS* 4.5 19.9 + - - -
386H ASP* 4.2 21.7 + - - +
389H LYS* 4.7 12.7 - - - +
437H LYS* 5.7 3.0 - - - +
349I ASN 4.1 2.7 - - - +
350I ASN* 2.7 48.3 + - - +
353I SER* 1.3 80.6 - - - +
355I ILE* 1.3 53.7 + - + +
357I LYS* 4.2 4.4 - - - +
358I THR* 2.3 41.9 + - - +
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Residues in contact with ILE 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305I ILE* 4.5 15.9 - - + -
309I MET* 3.9 28.5 - - + -
337I VAL* 4.7 22.7 - - + -
340I ILE* 6.2 1.6 - - + -
341I CYS* 4.8 4.5 - - - -
350I ASN* 4.2 3.8 - - - +
351I ILE* 3.0 40.2 + - + +
352I GLN* 5.2 0.2 - - - -
354I ARG* 1.3 77.3 - - + +
356I THR* 1.3 57.5 + - + +
358I THR* 3.3 6.7 - - - +
359I PHE* 2.9 54.2 + - + -
383I LEU* 5.2 8.5 - - + -
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Residues in contact with THR 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352I GLN* 2.3 39.0 + - + +
353I SER* 2.8 15.1 + - - -
355I ILE* 1.3 76.3 - - - +
357I LYS* 1.3 54.1 + - - +
359I PHE* 3.3 1.9 + - - +
360I THR* 2.3 39.5 + - - -
380I LEU* 4.5 12.3 - - + +
383I LEU* 3.7 26.7 - - + -
387I VAL* 5.4 5.4 - - + -
391I LEU* 5.7 2.9 - - + -
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Residues in contact with LYS 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437H LYS 5.7 2.6 + - - -
438H LEU* 4.7 18.4 + - - +
353I SER* 2.9 36.4 + - - +
354I ARG* 4.2 5.2 - - - +
356I THR* 1.3 75.8 + - - +
358I THR* 1.3 66.0 + - - +
360I THR* 3.3 9.6 - - + +
361I LYS* 3.0 39.0 + - + +
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Residues in contact with THR 358 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309I MET* 3.8 23.7 - - + +
313I VAL* 6.5 1.3 - - + -
354I ARG* 2.3 31.6 + - - +
355I ILE* 3.3 9.5 - - - -
357I LYS* 1.3 77.1 - - - +
359I PHE* 1.3 60.9 + - + +
361I LYS* 3.8 2.1 - - - +
362I SER* 2.3 42.6 + - - +
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Residues in contact with PHE 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309I MET* 3.6 28.7 - - + -
312I ILE* 4.2 35.0 - - + -
313I VAL* 5.7 6.3 - - + -
337I VAL* 5.5 4.7 - - + -
355I ILE* 2.9 32.6 + - + +
358I THR* 1.3 80.8 - - + +
360I THR* 1.3 60.0 + - - +
362I SER* 3.6 6.8 - - - -
363I TRP* 2.8 29.5 + - - +
375I GLY 4.5 0.9 - - - -
376I SER* 3.7 30.3 - - - +
379I GLY* 3.7 22.0 - - - -
380I LEU* 3.7 36.1 - - + +
383I LEU* 5.3 0.9 - - + -
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Residues in contact with THR 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I THR* 2.3 32.8 + - - -
357I LYS* 3.3 13.2 - - + +
358I THR 3.2 0.2 - - - -
359I PHE* 1.3 76.3 - - - +
361I LYS* 1.3 65.1 + - + +
363I TRP* 3.0 8.1 + - - +
364I VAL* 3.0 33.7 + - + +
380I LEU* 4.8 2.6 - - - +
391I LEU* 5.1 11.0 - - + +
395I ARG* 3.6 18.0 + - - +
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Residues in contact with LYS 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I LYS* 3.0 24.9 + - + +
358I THR* 4.3 1.8 - - - +
360I THR* 1.3 85.4 - - + +
362I SER* 1.3 57.8 + - - +
364I VAL* 3.4 14.8 + - + +
365I ASP* 3.0 33.4 + - - +
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Residues in contact with SER 362 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I THR* 2.3 35.9 + - - +
359I PHE* 3.6 12.6 - - - -
360I THR 3.1 0.2 - - - -
361I LYS* 1.3 75.6 - - - +
363I TRP* 1.3 63.0 + - - +
365I ASP* 3.2 29.6 + - - +
368I THR* 4.9 2.4 + - - -
372I THR* 5.4 9.2 + - - +
373I ARG* 5.3 4.3 + - - +
376I SER* 4.4 12.3 + - - -
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Residues in contact with TRP 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359I PHE 2.8 14.7 + - - +
360I THR 3.3 7.2 - - - +
362I SER* 1.3 76.3 - - - +
364I VAL* 1.3 70.4 + - + +
365I ASP 3.4 2.9 + - - +
373I ARG* 5.5 3.0 - - + +
376I SER* 4.6 8.0 - - - +
377I ILE* 3.5 19.9 - - + +
395I ARG* 3.3 43.3 - - + +
398I GLN* 3.2 33.0 - - + -
399I GLU* 2.4 44.8 + - + +
402I ARG* 2.5 76.8 + - - +
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Residues in contact with VAL 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360I THR* 3.0 21.5 + - + +
361I LYS* 3.5 18.8 - - + +
362I SER 3.2 0.4 - - - -
363I TRP* 1.3 92.5 - - + +
365I ASP* 1.3 60.1 + - - +
366I GLU* 2.9 15.1 + - - +
395I ARG* 5.0 0.4 - - - +
402I ARG* 4.4 3.7 + - - +
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Residues in contact with ASP 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361I LYS* 3.0 26.6 + - - +
362I SER* 3.3 22.3 + - - +
363I TRP 3.2 4.9 - - - +
364I VAL* 1.3 73.5 - - - +
366I GLU* 1.3 59.8 + - - +
368I THR* 3.1 36.5 + - + +
373I ARG* 3.2 8.3 + - - -
402I ARG* 5.5 0.6 + - - -
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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
------------------------------------------------------------
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