Contacts of the helix formed by residues 385 - 399 (chain W) in PDB entry 2GLJ
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 385 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81V ARG* 4.6 13.2 - - - +
83V LYS* 4.2 22.0 - - - +
240V GLU* 5.4 0.6 - - - +
302V ALA* 5.8 5.7 - - - +
303V THR* 5.6 1.9 + - - -
383W ASP 4.3 6.4 + - - +
384W ALA* 1.3 74.0 - - - +
386W PRO* 1.3 63.2 - - - +
387W GLU* 3.1 26.1 - - + +
388W TYR* 3.1 7.1 + - + +
389W ILE* 3.0 27.6 + - - +
428W MET 5.2 0.8 + - - -
429W GLN* 2.6 34.5 + - - +
430W VAL 4.7 1.4 + - - -
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Residues in contact with PRO 386 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83V LYS* 5.1 2.5 - - - +
150V VAL* 4.8 6.5 - - + -
152V VAL* 3.9 11.7 - - + -
238V SER* 3.3 29.1 - - - +
239V ALA 3.8 10.5 - - - +
240V GLU* 3.7 34.5 - - + +
371W LYS* 4.8 0.7 - - - -
384W ALA 3.7 4.2 - - - +
385W ASN* 1.3 78.0 - - + +
387W GLU* 1.3 83.9 + - - +
389W ILE* 3.0 12.7 + - + +
390W ALA* 2.7 32.9 + - - +
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Residues in contact with GLU 387 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81V ARG* 3.4 45.7 + - - +
83V LYS* 4.9 5.8 - - - -
150V VAL* 5.8 2.4 - - - +
152V VAL* 3.9 18.7 - - + +
158V ILE* 4.2 15.1 - - + +
385W ASN* 3.1 18.0 - - + +
386W PRO* 1.3 108.7 - - - +
388W TYR* 1.3 63.5 + - - +
390W ALA* 3.6 2.9 + - - +
391W GLU* 3.3 24.7 + - - +
429W GLN* 4.5 3.8 - - - +
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Residues in contact with TYR 388 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337W GLU* 3.6 30.1 - - + +
338W MET 2.9 18.1 + - - -
339W LEU* 3.7 1.7 - - - +
384W ALA* 5.2 0.9 - - + -
385W ASN* 3.1 12.6 + - + +
387W GLU* 1.3 78.8 - - - +
389W ILE* 1.3 67.0 + - - +
391W GLU* 3.2 13.3 + - + +
392W LEU* 3.1 36.2 + - + +
429W GLN* 3.0 59.5 + - + +
430W VAL 4.0 8.7 - - - -
431W ILE* 3.6 26.5 - - + -
462W PHE* 3.2 23.2 - + - -
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Residues in contact with ILE 389 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115V GLN* 4.9 1.3 - - - +
237V VAL* 3.6 40.4 - - + +
238V SER* 3.7 7.9 - - - -
369W PHE* 5.7 3.6 - - + -
371W LYS* 3.8 29.8 - - + -
384W ALA* 4.0 9.9 - - + +
385W ASN 3.0 22.3 + - - +
386W PRO* 3.4 9.9 - - + +
388W TYR* 1.3 73.2 - - + +
390W ALA* 1.3 67.5 + - - +
392W LEU* 3.0 13.5 + - + +
393W ARG* 2.9 23.4 + - + +
431W ILE* 3.5 27.4 - - + -
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Residues in contact with ALA 390 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152V VAL* 3.3 33.7 - - + -
153V LYS 3.5 13.7 - - - +
154V LYS* 4.1 6.2 - - - +
156V GLY* 5.3 2.0 - - - -
238V SER* 3.4 16.9 - - - +
386W PRO 2.7 13.8 + - - +
387W GLU 3.8 3.4 - - - +
389W ILE* 1.3 71.7 - - - +
391W GLU* 1.3 63.8 + - + +
393W ARG* 3.0 11.4 + - - +
394W ARG* 2.9 22.2 + - - +
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Residues in contact with GLU 391 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154V LYS 4.3 5.7 - - - +
155V ASP 5.2 4.3 - - - +
156V GLY* 5.5 3.1 + - - -
337W GLU* 5.6 4.7 - - - +
387W GLU 3.3 12.5 + - - +
388W TYR* 3.2 18.3 + - + +
389W ILE 3.1 0.2 - - - -
390W ALA* 1.3 79.7 - - + +
392W LEU* 1.3 62.7 + - + +
394W ARG* 3.1 50.7 + - - +
395W ILE* 2.9 34.1 + - + +
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Residues in contact with LEU 392 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339W LEU* 4.0 7.6 - - + -
369W PHE* 3.5 26.7 - - + -
388W TYR* 3.4 29.4 - - + +
389W ILE* 3.0 8.1 + - + +
391W GLU* 1.3 77.4 - - + +
393W ARG* 1.3 56.7 + - - +
395W ILE* 3.6 10.2 - - + +
396W LEU* 2.8 41.0 + - + +
431W ILE* 3.5 38.4 - - + -
462W PHE* 3.6 36.3 - - + -
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Residues in contact with ARG 393 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152V VAL 3.6 3.4 + - - -
153V LYS 4.8 0.2 - - - -
154V LYS* 4.0 26.5 - - + +
232V SER* 5.0 0.4 + - - -
234V GLU* 2.6 45.1 + - - +
235V ASP* 2.6 41.6 + - - +
237V VAL* 4.5 6.3 - - + -
238V SER* 2.6 49.8 + - - +
389W ILE* 2.9 20.1 + - + +
390W ALA* 3.0 8.5 - - - +
392W LEU* 1.3 79.8 - - - +
394W ARG* 1.3 60.0 + - - +
396W LEU* 3.1 11.2 + - - -
397W SER* 2.7 24.5 + - - -
403W TRP* 4.3 19.3 + - + +
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Residues in contact with ARG 394 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154V LYS* 3.6 42.5 - - + +
155V ASP* 5.2 8.3 + - - +
390W ALA 2.9 3.5 + - - +
391W GLU* 3.1 44.1 + - - +
393W ARG* 1.3 79.6 - - - +
395W ILE* 1.3 70.1 + - - +
397W SER* 3.0 16.8 + - - -
398W LYS* 3.2 10.3 + - + +
465W ASN* 3.7 25.5 + - - +
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Residues in contact with ILE 395 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100W LYS* 5.0 6.5 - - - +
391W GLU* 2.9 25.7 + - + +
392W LEU* 3.6 19.7 - - + +
394W ARG* 1.3 82.2 - - - +
396W LEU* 1.3 57.2 + - + +
397W SER 2.7 15.3 + - - -
398W LYS* 3.2 13.4 + - - +
399W GLU* 3.3 15.8 + - + +
461W ALA* 2.8 31.4 - - + +
462W PHE* 4.7 11.0 - - + -
464W ASN 4.7 0.2 - - - +
465W ASN* 3.1 41.3 - - - +
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Residues in contact with LEU 396 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339W LEU* 6.5 0.7 - - + -
367W ILE* 4.7 3.6 - - + -
369W PHE* 3.5 38.8 - - + -
392W LEU* 2.8 26.9 + - + +
393W ARG* 3.4 5.2 - - - +
395W ILE* 1.3 74.0 - - + +
397W SER* 1.3 54.6 + - - +
400W SER 2.3 26.9 - - - +
401W VAL* 3.3 24.6 - - + +
403W TRP* 4.2 25.6 + - + +
458W GLY* 3.4 39.9 - - - +
461W ALA* 4.3 8.5 - - + +
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Residues in contact with SER 397 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154V LYS* 3.2 28.7 + - - -
393W ARG 2.7 15.4 + - - -
394W ARG* 3.1 12.3 - - - -
395W ILE 2.7 0.6 + - - -
396W LEU* 1.3 81.0 + - - +
398W LYS* 1.3 70.3 + - - +
400W SER* 2.9 14.7 + - - +
403W TRP* 4.9 5.0 + - - -
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Residues in contact with LYS 398 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394W ARG* 3.2 7.8 + - + +
395W ILE* 3.8 8.7 - - - +
397W SER* 1.3 78.2 - - - +
399W GLU* 1.3 98.8 + - + +
400W SER* 2.8 10.9 + - - -
465W ASN* 4.8 24.0 - - + +
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Residues in contact with GLU 399 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395W ILE* 3.3 10.3 + - + +
398W LYS* 1.3 106.5 + - + +
400W SER* 1.3 70.9 + - - +
401W VAL* 3.5 8.1 + - + +
461W ALA* 3.6 37.2 - - + +
463W LEU* 4.9 8.9 - - + +
464W ASN 5.7 3.1 - - - +
465W ASN* 5.7 1.6 - - + +
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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
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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