Contacts of the helix formed by residues 387 - 398 (chain B) in PDB entry 5Y7G
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 387 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B VAL* 3.7 5.3 + - - +
386B GLU* 1.3 89.1 + - - +
388B GLY* 1.3 63.2 + - - +
389B LEU 3.3 2.2 - - - +
390B ILE* 4.3 4.6 - - - +
391B ASN* 2.7 44.5 + - - +
466B TYR* 4.2 10.2 + - - -
502B ARG 3.8 11.7 - - - +
503B ALA* 3.7 22.3 - - - +
504B GLY 3.9 5.7 - - - +
505B LEU* 3.3 48.9 + - + +
506B PRO 3.9 0.4 + - - -
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Residues in contact with GLY 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B VAL* 3.5 6.7 - - - +
386B GLU 2.5 14.5 + - - -
387B ASN* 1.3 76.3 - - - +
389B LEU* 1.3 55.1 + - - +
392B SER* 2.4 38.2 + - - -
466B TYR* 3.5 23.6 - - - -
469B LEU* 4.4 13.7 - - - -
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B VAL* 3.1 23.7 - - + +
388B GLY* 1.3 74.2 - - - +
390B ILE* 1.3 65.3 + - + +
392B SER* 4.2 2.2 - - - -
393B LEU* 2.9 52.6 + - + +
470B LEU* 3.7 28.7 - - + -
474B LEU* 3.7 27.6 - - + -
478B ALA* 4.1 19.5 - - + -
482B LEU* 5.0 5.4 - - + -
509B ILE* 3.4 25.8 - - + -
511B PHE* 4.1 7.0 - - + -
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B VAL* 4.7 1.3 - - + -
387B ASN* 4.1 6.0 + - - +
389B LEU* 1.3 80.6 - - + +
391B ASN* 1.3 67.3 + - - +
393B LEU* 4.0 4.2 - - - -
394B PHE* 3.0 23.4 + - - +
482B LEU* 6.3 1.8 - - + -
487B LEU* 5.9 1.3 - - + -
490B TRP* 3.8 47.6 - - + +
491B PHE* 3.6 9.7 - - + -
494B LEU* 5.0 6.5 - - + -
505B LEU* 3.6 35.9 - - + -
506B PRO* 5.8 0.2 - - + -
509B ILE* 4.2 23.1 - - + -
520B MET* 4.4 21.3 - - + -
537B TRP* 5.4 2.5 - - + -
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ASN* 2.7 34.4 + - - +
389B LEU 3.3 0.2 - - - -
390B ILE* 1.3 78.4 - - - +
392B SER* 1.3 62.0 + - - +
394B PHE* 3.1 4.0 + - - +
395B GLY 2.9 19.9 + - - -
464B PHE* 3.2 36.2 - - - +
466B TYR* 3.7 14.2 + - + -
494B LEU* 3.8 17.3 - - - +
502B ARG* 3.1 44.0 + - - +
505B LEU* 5.1 2.8 - - - +
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLY 2.4 26.8 + - - -
389B LEU* 3.7 6.3 - - - -
390B ILE 3.2 0.4 - - - -
391B ASN* 1.3 76.3 - - - +
393B LEU* 1.3 58.8 + - - +
395B GLY* 3.1 2.3 + - - -
396B LEU* 2.8 35.8 + - - +
464B PHE 3.2 7.4 - - - -
465B VAL* 4.1 5.2 - - - +
466B TYR* 2.9 30.6 + - - +
470B LEU* 3.8 25.2 - - - +
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 2.9 38.5 + - + +
390B ILE* 4.0 3.1 - - - +
392B SER* 1.3 74.9 - - - +
394B PHE* 1.3 64.6 + - - +
396B LEU* 3.8 5.4 - - + +
397B LEU* 3.0 25.8 + - - +
450B ILE* 4.1 18.4 - - + +
470B LEU* 5.3 0.9 - - + -
475B LEU* 4.0 16.6 - - + -
478B ALA* 4.1 6.1 - - + -
479B LEU* 3.9 25.6 - - + -
482B LEU* 3.7 30.3 - - + -
487B LEU* 4.3 12.3 - - + -
491B PHE* 3.8 13.4 - - + -
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Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B ILE 3.0 10.1 + - - +
391B ASN 3.4 6.3 - - - +
393B LEU* 1.3 78.5 - - - +
395B GLY* 1.3 59.9 + - - +
397B LEU* 3.8 1.0 - - - +
398B CYS* 2.9 51.8 + - + +
402B ILE* 4.0 6.3 - - + -
426B PHE* 6.1 0.2 - + - -
434B PHE* 3.7 26.5 - + - -
438B LEU* 5.0 0.4 - - + -
464B PHE* 3.5 38.1 - + - -
491B PHE* 3.4 46.7 - + + -
494B LEU* 3.9 23.1 - - + -
495B LEU* 3.8 25.4 - - + -
498B ILE* 5.7 2.2 - - + -
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Residues in contact with GLY 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B ASN 2.9 17.3 + - - -
392B SER 3.6 2.9 - - - -
394B PHE* 1.3 73.7 - - - +
396B LEU* 1.3 60.3 + - - +
398B CYS 3.9 0.2 - - - -
399B TRP* 3.2 30.9 + - - -
402B ILE* 4.0 18.8 - - - +
464B PHE* 4.0 14.4 - - - -
465B VAL* 4.0 9.9 - - - -
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Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B SER 2.8 19.4 + - - +
393B LEU* 3.8 5.2 - - - +
395B GLY* 1.3 79.7 - - - +
397B LEU* 1.3 62.8 + - - +
399B TRP* 3.4 10.1 + - + +
450B ILE* 4.2 27.4 - - + -
453B ARG* 3.3 32.6 - - + +
454B TYR* 4.0 27.1 - - + +
465B VAL* 4.0 10.3 - - + -
467B TRP* 3.8 29.4 - - + -
470B LEU* 3.5 32.5 - - + -
475B LEU* 4.4 1.8 - - + -
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B LEU 3.0 17.9 + - - +
394B PHE* 3.9 3.6 - - - +
396B LEU* 1.3 78.6 - - - +
398B CYS* 1.3 60.6 + - - +
399B TRP 3.3 1.8 + - - -
437B CYS* 3.1 44.1 - - - +
438B LEU* 4.5 2.9 - - - -
440B ARG* 4.2 8.7 - - + +
441B LEU* 4.0 25.4 - - + +
446B TYR* 4.2 24.7 - - + +
449B ALA* 4.3 9.6 - - + -
450B ILE* 3.9 24.0 - - + +
453B ARG* 3.9 9.4 + - - +
487B LEU* 6.3 0.2 - - + -
491B PHE* 4.5 13.7 - - + -
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Residues in contact with CYS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B PHE* 2.9 41.6 + - + +
395B GLY 3.9 2.0 - - - -
397B LEU* 1.3 79.0 - - - +
399B TRP* 1.3 65.5 + - - +
400B GLU 3.1 3.4 - - - -
401B ALA* 2.8 14.2 + - + -
402B ILE* 3.0 15.0 + - + +
434B PHE* 3.8 27.6 - - + -
437B CYS* 3.7 23.6 - - + -
438B LEU* 4.1 16.8 - - - -
491B PHE* 5.5 0.2 - - - -
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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