Contacts of the helix formed by residues 369 - 383 (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 PRO 369 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314I SER* 5.6 0.4 - - - -
315I ARG* 5.0 21.3 - - + +
367I LYS 4.9 0.7 - - - +
368I THR* 1.3 87.0 - - + +
370I TRP* 1.3 62.9 + - + +
371I THR* 3.1 19.5 - - + -
372I THR* 2.3 45.3 + - + -
373I ARG* 3.3 0.6 - - - -
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Residues in contact with TRP 370 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I TRP* 4.6 4.4 - - + -
368I THR 4.6 2.8 + - - -
369I PRO* 1.3 72.4 - - + +
371I THR* 1.3 59.7 + - - +
372I THR 3.2 0.4 - - - -
373I ARG* 3.2 55.4 + - + +
374I TYR* 2.8 30.4 + - - +
402I ARG* 4.5 25.8 - - + -
405I SER* 4.8 3.6 - - - -
406I VAL* 3.5 25.4 - - + +
416I ASP* 4.7 19.9 + - + +
419I GLY 5.4 1.1 - - - -
420I ALA* 3.7 35.4 - - + +
423I VAL* 4.6 9.2 - - + +
424I GLN* 4.3 13.7 - - + -
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Residues in contact with THR 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313I VAL 3.0 12.0 + - - +
314I SER* 3.4 7.5 - - - -
315I ARG* 3.7 21.1 - - + +
317I LEU* 6.2 3.4 - - + -
327I TRP* 4.0 19.8 - - - -
330I ARG* 2.7 40.8 + - - -
369I PRO* 3.7 22.4 - - + -
370I TRP* 1.3 76.7 - - - +
372I THR* 1.3 60.3 + - - +
374I TYR* 3.8 1.2 - - - +
375I GLY* 2.9 25.1 + - - -
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Residues in contact with THR 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313I VAL* 3.2 20.7 - - + +
314I SER* 3.6 26.2 - - - -
362I SER* 5.4 9.2 + - - -
368I THR* 3.1 22.0 + - - -
369I PRO* 2.3 38.8 + - + +
371I THR* 1.3 77.8 - - + +
373I ARG* 1.3 61.9 + - - +
375I GLY* 3.9 0.5 - - - -
376I SER* 2.9 32.3 + - - -
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Residues in contact with ARG 373 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362I SER 5.3 6.8 + - - +
363I TRP* 5.5 1.1 - - + +
365I ASP 3.2 11.5 + - - -
366I GLU* 3.6 4.8 - - - +
367I LYS* 3.1 31.1 - - - +
368I THR* 2.4 34.8 + - - +
369I PRO 3.3 7.6 - - - -
370I TRP* 3.2 66.4 + - + +
372I THR* 1.3 98.1 + - - +
374I TYR* 1.3 58.3 + - - +
376I SER* 2.5 22.4 + - - -
377I ILE* 3.0 28.7 + - + +
402I ARG* 4.1 22.6 - - - +
423I VAL* 5.6 2.2 - - + -
427I LEU* 5.0 0.7 - - - -
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Residues in contact with TYR 374 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I TRP* 3.4 44.6 + + + +
330I ARG* 3.5 19.7 - - + -
331I ASP* 2.3 35.6 + - - -
370I TRP 2.8 17.1 + - - +
371I THR 3.8 2.7 - - - +
373I ARG* 1.3 77.6 - - - +
375I GLY* 1.3 56.3 + - - +
378I ALA* 2.9 38.0 + - + +
423I VAL* 3.5 31.4 - - + +
426I LEU* 3.6 33.4 - - + +
427I LEU* 3.7 30.4 - - + +
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Residues in contact with GLY 375 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312I ILE* 3.6 37.3 - - - +
313I VAL* 5.2 0.4 - - - -
330I ARG* 4.4 9.4 - - - -
334I ALA* 5.1 0.7 - - - +
359I PHE* 4.5 0.3 - - - -
371I THR 2.9 16.7 + - - -
372I THR 3.9 0.7 - - - -
374I TYR* 1.3 77.5 - - - +
376I SER* 1.3 57.3 + - - +
378I ALA* 3.9 4.0 - - - +
379I GLY* 2.9 25.3 + - - -
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Residues in contact with SER 376 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312I ILE* 4.5 0.2 - - - +
313I VAL* 6.3 0.2 - - - +
359I PHE* 3.7 40.0 - - - -
362I SER* 4.4 10.8 - - - -
363I TRP* 4.6 7.7 - - - -
372I THR 2.9 15.6 + - - -
373I ARG* 2.5 27.5 + - - -
375I GLY* 1.3 77.0 - - - +
377I ILE* 1.3 64.5 + - - +
379I GLY 3.2 2.1 + - - -
380I LEU* 2.9 34.3 + - - +
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Residues in contact with ILE 377 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363I TRP* 3.5 22.0 - - + +
373I ARG* 3.0 25.4 + - + +
376I SER* 1.3 86.1 + - - +
378I ALA* 1.3 58.2 + - - +
380I LEU* 3.3 6.9 + - - +
381I ALA* 2.8 28.6 + - + +
388I ILE* 4.9 2.3 - - + +
392I ILE* 4.9 13.0 - - + -
395I ARG* 4.8 5.2 - - - +
399I GLU* 3.5 30.1 - - + +
402I ARG* 5.1 1.1 - - - +
427I LEU* 3.8 33.7 - - + -
431I CYS* 6.5 0.4 - - + -
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Residues in contact with ALA 378 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330I ARG 5.0 3.1 - - - +
331I ASP* 4.8 8.1 - - - +
334I ALA* 3.9 12.1 - - + -
374I TYR* 2.9 33.2 + - + +
375I GLY* 3.9 4.9 - - - +
377I ILE* 1.3 74.8 - - - +
379I GLY* 1.3 60.1 + - - +
381I ALA* 3.1 8.9 + - - +
382I GLU* 2.9 32.5 + - + +
427I LEU* 4.2 13.3 - - + +
430I HIS* 6.0 0.4 - - - -
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Residues in contact with GLY 379 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312I ILE* 5.8 1.3 - - - -
334I ALA* 3.7 17.1 - - - +
337I VAL* 5.6 5.7 - - - +
359I PHE* 3.7 23.1 - - - -
375I GLY 2.9 13.1 + - - -
376I SER 3.7 3.1 - - - -
378I ALA* 1.3 76.3 - - - +
380I LEU* 1.3 60.6 + - - +
382I GLU* 3.3 11.5 + - - +
383I LEU* 3.3 17.5 + - - +
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Residues in contact with LEU 380 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I THR* 4.5 13.2 - - + +
359I PHE* 3.7 33.0 - - + +
360I THR* 4.8 1.8 - - - +
376I SER* 2.9 23.6 + - - +
377I ILE* 3.7 8.3 - - + +
379I GLY* 1.3 73.2 - - - +
381I ALA* 1.3 64.2 + - - +
383I LEU* 3.3 28.5 + - + -
384I GLY 4.0 0.5 + - - -
387I VAL* 3.5 12.3 - - - +
388I ILE* 3.3 17.8 - - + +
391I LEU* 3.7 29.4 - - + -
392I ILE* 5.6 2.2 - - + -
395I ARG* 3.4 29.2 - - - +
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Residues in contact with ALA 381 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I ILE* 2.8 19.5 + - + +
378I ALA* 3.1 10.1 + - - +
380I LEU* 1.3 77.4 - - - +
382I GLU* 1.3 61.3 + - + +
383I LEU 3.3 0.9 + - - -
384I GLY* 3.4 15.2 + - - +
388I ILE* 3.7 16.5 - - + +
427I LEU* 5.4 2.0 - - + -
430I HIS* 3.5 36.0 + - + +
431I CYS* 6.3 1.1 - - - -
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Residues in contact with GLU 382 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331I ASP 4.6 2.6 - - - +
334I ALA* 3.3 32.1 - - + +
335I ARG* 3.4 26.5 - - - +
337I VAL* 6.0 0.4 - - + -
338I ALA* 3.3 36.0 - - + +
342I LYS* 6.1 0.7 - - - -
378I ALA* 2.9 19.2 + - + +
379I GLY 3.8 5.4 - - - +
380I LEU 3.3 0.4 - - - -
381I ALA* 1.3 77.9 - - + +
383I LEU* 1.3 62.6 + - - +
384I GLY* 3.2 1.5 + - - -
430I HIS* 4.7 13.5 + - - +
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Residues in contact with LEU 383 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I VAL* 5.3 4.7 - - + -
338I ALA* 5.4 2.5 - - - -
341I CYS* 3.6 35.2 - - + -
342I LYS* 6.2 0.3 - - - -
352I GLN* 5.8 7.2 - - + -
355I ILE* 5.2 10.3 - - + -
356I THR* 3.7 31.4 - - + -
379I GLY 3.3 12.3 - - - +
380I LEU* 3.3 28.5 + - + +
381I ALA 3.2 1.4 - - - -
382I GLU* 1.3 78.8 - - - +
384I GLY* 1.3 57.5 + - - +
387I VAL* 3.6 24.7 - - + +
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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