Contacts of the helix formed by residues 379 - 391 (chain A) in PDB entry 2YEV
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 SER 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A GLN 4.4 0.4 - - - -
376A PHE* 2.7 23.9 + - - -
378A ASP* 1.3 80.6 - - - +
380A TYR* 1.3 65.4 + - - +
381A PHE* 3.2 16.3 + - - +
382A VAL* 3.1 15.8 + - - +
383A VAL* 3.5 9.5 + - - +
441A GLY* 3.9 9.2 + - - -
445A MET 3.3 13.0 - - - -
446A PRO* 4.0 0.2 - - - -
447A ARG* 3.8 6.4 - - - +
165B TRP* 3.7 24.0 - - - -
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Residues in contact with TYR 380 (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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49A ILE* 5.4 1.0 - - - +
50A ARG* 4.5 4.0 + - - -
53A LEU* 3.3 27.4 - - + +
66A TYR* 4.4 5.5 + - - -
379A SER* 1.3 69.1 - - - +
381A PHE* 1.3 58.9 + - - +
382A VAL 3.2 0.2 - - - -
383A VAL* 3.5 22.4 - - + +
384A ALA* 2.8 30.1 + - - +
437A GLN* 3.5 57.2 - - + +
440A LEU* 4.0 12.3 - - + -
441A GLY* 4.1 1.7 - - - +
445A MET* 2.9 42.5 + - + +
446A PRO 3.5 26.9 - - - -
447A ARG* 3.9 11.0 - - + -
448A ARG 4.8 4.5 + - - -
449A TYR 5.2 3.2 + - - -
463A ASN* 5.5 0.9 - - - -
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Residues in contact with PHE 381 (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 THR* 3.8 35.0 - - + -
366A MET* 3.6 24.5 - - + -
367A LEU* 3.5 31.6 - - + -
376A PHE* 3.4 33.4 - + + -
379A SER* 3.1 13.8 + - - +
380A TYR* 1.3 76.0 - - - +
382A VAL* 1.3 56.4 + - - +
384A ALA* 3.3 2.4 + - - +
385A HIS* 2.9 24.8 + - - +
437A GLN 4.3 3.1 - - - -
438A TYR* 3.6 29.5 - + + -
441A GLY* 3.6 11.2 - - - -
442A TYR* 3.7 26.9 - + - -
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Residues in contact with VAL 382 (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 LEU* 3.8 27.8 - - + -
373A ASP* 4.9 1.6 - - - +
376A PHE 3.4 23.3 - - - +
377A HIS* 4.2 4.9 - - - +
378A ASP 4.1 9.2 - - - +
379A SER 3.1 8.8 + - - +
381A PHE* 1.3 75.3 - - - +
383A VAL* 1.3 64.7 + - - +
385A HIS* 3.1 10.1 + - + +
386A PHE* 2.9 41.9 + - + -
447A ARG* 3.9 19.3 - - - +
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A SER 3.8 6.1 - - - +
380A TYR* 3.2 26.2 + - + +
382A VAL* 1.3 76.6 - - - +
384A ALA* 1.3 60.4 + - - +
386A PHE* 3.4 14.1 + - + -
387A HIS* 2.8 52.6 + - + -
437A GLN* 3.4 17.9 - - - +
447A ARG* 3.6 41.5 - - + +
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Residues in contact with ALA 384 (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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380A TYR 2.8 19.1 + - - +
381A PHE 3.6 0.2 - - - +
383A VAL* 1.3 71.3 - - - +
385A HIS* 1.3 65.8 + - - +
387A HIS* 3.4 0.7 + - - +
388A ASN* 2.9 25.1 + - - +
430A TYR* 4.9 0.3 + - - -
434A PHE* 3.6 18.6 - - - +
437A GLN* 4.0 7.4 + - + -
438A TYR* 3.4 49.1 + - + +
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Residues in contact with HIS 385 (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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360A GLY 3.0 23.7 + - - -
361A GLY* 5.2 1.1 - - - -
363A THR* 3.5 8.9 + - - +
364A GLY* 3.3 27.3 + - - -
367A LEU* 3.6 27.3 - - + +
381A PHE* 2.9 15.0 + - + +
382A VAL* 3.1 9.8 + - + +
384A ALA* 1.3 75.7 - - - +
386A PHE* 1.3 72.4 + + + +
388A ASN* 3.1 20.6 + - - +
389A VAL* 3.1 23.0 + - + +
438A TYR* 3.5 12.0 - - - -
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Residues in contact with PHE 386 (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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139A TRP* 6.2 0.9 - - - -
382A VAL* 2.9 37.3 + - + +
383A VAL* 3.5 25.4 - - + -
385A HIS* 1.3 82.9 - - + +
387A HIS* 1.3 91.2 + + - +
389A VAL* 3.8 8.5 - - + -
390A LEU* 2.8 54.3 + - + +
447A ARG* 3.9 28.5 - - - -
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Residues in contact with HIS 387 (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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73A HIS* 4.1 22.7 + + - -
383A VAL* 2.8 43.5 + - + +
384A ALA 4.2 0.2 - - - +
386A PHE* 1.3 100.1 - + - +
388A ASN* 1.3 61.6 + - - +
390A LEU* 4.6 2.7 - - + -
391A MET* 2.8 41.3 + - + +
392A ALA 3.3 2.6 + - - -
430A TYR* 3.9 2.7 - - - -
434A PHE* 3.2 48.7 - + + -
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Residues in contact with ASN 388 (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 ASN* 3.0 23.9 - - - +
357A PHE* 5.2 0.9 - - - -
359A LEU* 3.5 17.4 - - - +
360A GLY* 3.3 22.2 + - - +
384A ALA 2.9 14.8 + - - +
385A HIS 3.1 13.5 - - - +
387A HIS* 1.3 79.1 - - - +
389A VAL* 1.3 55.0 + - - +
392A ALA* 3.5 5.2 - - - +
393A GLY* 3.3 18.4 + - - -
430A TYR* 2.7 29.5 + - - +
438A TYR* 2.7 25.0 + - - +
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Residues in contact with VAL 389 (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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257A LEU* 5.3 0.7 - - + +
357A PHE* 3.7 30.3 - - + -
360A GLY* 3.6 36.1 - - - +
361A GLY* 4.0 2.2 - - - +
385A HIS* 3.1 26.6 + - + +
386A PHE* 3.6 13.5 - - + +
388A ASN* 1.3 76.9 - - - +
390A LEU* 1.3 66.3 + - + +
393A GLY* 3.4 5.8 - - - +
394A SER* 3.0 25.8 + - - -
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Residues in contact with LEU 390 (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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78A LEU* 3.8 22.9 - - + -
81A PHE* 5.8 0.5 - - - -
82A ILE* 4.1 15.6 - - + +
253A VAL* 5.4 11.4 - - + +
256A MET* 3.8 29.6 - - + -
386A PHE* 2.8 48.6 + - + +
387A HIS* 4.6 3.6 - - + -
389A VAL* 1.3 79.8 - - + +
391A MET* 1.3 54.5 + - + +
394A SER* 3.6 13.2 - - - +
395A GLY* 2.8 27.2 + - - -
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Residues in contact with MET 391 (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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39A PHE* 4.5 20.6 - - + -
387A HIS* 2.8 33.2 + - + +
390A LEU* 1.3 71.8 - - - +
392A ALA* 1.3 59.7 + - - +
393A GLY 3.1 3.3 + - - -
395A GLY* 3.3 8.2 - - - +
396A PHE* 3.0 36.9 + - + -
399A PHE* 6.4 0.2 - - - -
426A PHE* 3.9 28.0 - - + +
430A TYR* 4.2 15.9 - - + -
434A PHE* 4.4 9.9 - - + -
473A LEU* 3.9 36.1 - - + -
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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