Contacts of the helix formed by residues 359 - 373 (chain A) in PDB entry 5V5Z
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 LEU 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A GLU* 3.3 46.2 - - + +
337A VAL* 3.8 17.7 - - + +
340A LEU* 3.5 16.8 - - + -
351A LEU* 3.8 25.1 - - + -
355A ASP 3.4 19.3 - - - +
356A LEU* 3.5 10.6 + - + +
357A GLN 3.6 0.8 + - - -
358A LYS* 1.3 75.0 - - - +
360A PRO* 1.3 63.1 - - - +
361A SER 3.3 2.7 - - - -
362A VAL* 3.1 33.0 + - + +
363A ASN* 3.4 10.6 + - - +
485A THR* 4.4 12.8 - - + -
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Residues in contact with PRO 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLU* 3.1 22.7 - - + +
358A LYS 3.4 9.4 - - - +
359A LEU* 1.3 84.2 - - - +
361A SER* 1.3 57.9 + - - -
363A ASN* 3.8 11.9 - - + +
364A ASN* 2.7 49.8 + - - +
428A ASP* 5.3 3.1 - - - +
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Residues in contact with SER 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL* 3.6 21.0 - - - +
333A ILE* 3.5 25.8 - - - -
336A GLU* 2.0 46.0 + - - +
360A PRO* 1.3 75.3 - - - +
362A VAL* 1.3 55.7 + - - +
364A ASN* 4.9 1.6 - - - +
365A THR* 2.4 42.1 + - - -
424A PRO* 4.9 2.8 - - - +
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE* 3.5 26.2 - - + +
336A GLU* 6.2 0.4 - - + -
337A VAL* 5.1 0.9 - - + -
356A LEU* 5.6 4.5 - - + +
359A LEU* 3.1 26.4 + - + +
361A SER* 1.3 76.8 - - - +
363A ASN* 1.3 62.9 + - - +
365A THR* 3.5 2.1 - - - -
366A ILE* 2.9 39.6 + - + +
481A GLY* 3.8 35.4 - - - +
484A LEU* 4.3 8.5 - - + -
485A THR* 3.5 24.9 - - + -
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Residues in contact with ASN 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A LEU* 3.1 28.6 + - - +
357A GLN* 4.5 15.4 + - - +
359A LEU 3.4 14.3 + - - +
360A PRO* 3.6 7.3 + - + +
361A SER 3.3 0.2 - - - -
362A VAL* 1.3 84.6 - - - +
364A ASN* 1.3 57.0 + - - +
366A ILE* 3.4 2.0 + - - +
367A LYS* 2.6 35.5 + - - +
477A TYR* 3.6 35.6 - - + +
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Residues in contact with ASN 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A PRO* 2.7 37.0 + - - +
361A SER* 4.3 2.0 - - - +
363A ASN* 1.3 77.8 - - - +
365A THR* 1.3 54.9 + - - +
367A LYS* 3.4 10.8 - - - +
368A GLU* 2.4 40.9 + - - +
424A PRO* 3.1 23.7 + - + +
425A THR* 5.6 0.4 - - - +
427A TRP* 3.2 28.3 - - + +
428A ASP* 3.7 22.4 + - - -
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A PHE* 4.0 10.5 - - + -
323A LEU* 4.3 16.3 - - + +
329A LEU* 5.5 1.9 + - - +
333A ILE* 4.7 5.9 - - - +
361A SER* 2.4 28.2 + - - -
362A VAL 3.5 4.7 - - - -
364A ASN* 1.3 74.3 - - - +
366A ILE* 1.3 51.0 + - - +
368A GLU* 3.6 0.9 - - - +
369A THR* 2.5 49.5 + - - +
422A PHE* 4.0 12.1 - - + -
424A PRO* 3.9 20.6 - - - +
484A LEU* 3.9 21.3 - - + -
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Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A THR* 4.4 3.1 - - + -
319A PHE* 4.1 8.5 - - + -
362A VAL* 2.9 28.7 + - + +
363A ASN* 3.6 4.3 - - - +
365A THR* 1.3 74.6 - - - +
367A LYS* 1.3 63.1 + - - +
369A THR* 3.3 5.9 + - - -
370A LEU* 3.0 30.9 + - + +
477A TYR* 3.7 36.3 - - + +
480A LEU* 3.5 31.4 - - + -
481A GLY* 3.5 35.4 - - - +
484A LEU* 4.1 11.7 - - + -
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Residues in contact with LYS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A ASN 2.6 22.3 + - - +
364A ASN* 3.4 14.1 - - - +
366A ILE* 1.3 73.9 - - - +
368A GLU* 1.3 60.2 + - - +
371A ARG* 3.1 10.4 + - - +
427A TRP* 3.8 33.2 - - + -
460A TYR* 2.5 61.1 + - + +
477A TYR* 3.5 17.2 + - + +
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ASN 2.4 30.4 + - - +
365A THR* 3.7 3.8 - - - +
367A LYS* 1.3 65.1 - - - +
369A THR* 1.3 66.2 + - - +
370A LEU 3.0 2.0 - - - -
371A ARG* 2.7 41.8 + - - +
372A MET* 2.9 22.5 + - - +
422A PHE* 3.9 17.5 - - + -
423A ASP 2.6 47.0 + - - +
424A PRO* 3.9 9.4 - - + -
426A ARG* 2.8 12.9 + - - -
427A TRP* 3.3 16.1 + - - +
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Residues in contact with THR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A THR* 3.5 33.0 + - + +
318A TRP* 3.6 14.6 - - + -
319A PHE* 3.1 33.0 - - + +
365A THR 2.5 29.6 + - - -
366A ILE* 3.8 6.5 - - - -
368A GLU* 1.3 73.7 - - - +
370A LEU* 1.3 56.2 + - - +
372A MET* 4.7 1.8 - - - +
373A HIS* 3.0 31.2 + - + +
422A PHE* 3.5 17.3 - - + -
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Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A THR* 3.8 23.6 - - + +
366A ILE* 3.0 31.1 + - + +
368A GLU 3.0 0.2 - - - -
369A THR* 1.3 74.5 - - - +
371A ARG* 1.3 66.1 + - - +
373A HIS 4.4 2.2 - - - +
374A MET* 3.1 27.2 + - - +
375A PRO* 3.9 11.7 - - + -
410A HIS* 4.0 3.1 + - - -
460A TYR* 3.7 13.9 - - - +
462A PRO* 4.2 11.4 - - + -
463A PHE* 3.8 26.0 - - + -
477A TYR* 3.8 15.3 - - + +
480A LEU* 5.1 0.2 - - + -
601A HEM 3.7 35.2 - - + -
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Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A LYS 3.1 8.4 + - - +
368A GLU* 2.7 47.5 + - - +
370A LEU* 1.3 78.7 - - - +
372A MET* 1.3 74.3 + - - +
373A HIS 3.1 1.0 + - - -
374A MET 4.0 2.3 + - - -
410A HIS* 3.0 63.5 + - + +
411A THR* 3.9 10.1 - - - +
416A PHE* 3.7 28.1 - - + +
419A PRO* 3.2 33.4 + - - +
421A ASP 3.2 15.8 + - - -
426A ARG* 3.4 15.3 - - - +
427A TRP* 3.8 7.6 - - + -
460A TYR* 3.6 25.7 - - + -
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Residues in contact with MET 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A HIS* 3.5 28.7 - - + +
326A LYS* 6.0 0.2 - - - +
368A GLU* 2.9 17.0 + - - +
369A THR 4.4 0.9 - - - +
371A ARG* 1.3 94.7 - - - +
373A HIS* 1.3 85.8 + - + +
374A MET 3.9 0.2 - - - -
411A THR* 4.3 16.8 - - + +
419A PRO 3.8 7.4 - - - +
420A GLU* 3.6 20.0 - - - +
422A PHE* 3.5 43.3 - - + -
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Residues in contact with HIS 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A SER* 5.1 1.0 + - - -
315A THR* 4.8 4.2 + - - -
318A TRP* 3.4 66.0 + + + +
322A HIS* 3.2 35.0 + + - -
369A THR* 3.0 18.4 + - + +
370A LEU* 3.6 4.3 - - - -
372A MET* 1.3 102.0 + - + +
374A MET* 1.3 68.7 + - - +
375A PRO* 3.3 9.4 - - - +
500A VAL* 5.1 1.0 - - + +
503A PRO* 4.3 15.2 - - + +
510A VAL* 5.6 5.4 - - + +
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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