Contacts of the helix formed by residues 385 - 399 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383R ASP 4.3 6.9 + - - +
384R ALA* 1.3 73.8 - - - +
386R PRO* 1.3 63.6 - - - +
387R GLU* 3.1 25.2 - - + +
388R TYR* 3.1 8.6 + - + +
389R ILE* 2.9 27.0 + - - +
428R MET 5.2 1.2 + - - -
429R GLN* 2.6 36.0 + - - +
430R VAL 4.7 1.8 + - - +
81T ARG* 4.4 13.2 - - - +
83T LYS* 4.2 22.0 - - - +
302T ALA* 5.8 5.7 - - - +
303T THR* 5.4 2.9 + - - +
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Residues in contact with PRO 386 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371R LYS* 4.9 0.9 - - - -
384R ALA 3.8 3.5 - - - +
385R ASN* 1.3 80.1 - - + +
387R GLU* 1.3 81.6 + - - +
389R ILE* 2.9 13.4 + - + +
390R ALA* 2.7 35.7 + - - +
83T LYS* 5.0 3.1 - - - +
150T VAL* 4.8 7.2 - - + +
152T VAL* 3.9 12.1 - - + -
238T SER* 3.4 26.4 - - - +
239T ALA 3.9 10.5 - - - +
240T GLU* 3.7 32.5 - - + +
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Residues in contact with GLU 387 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385R ASN* 3.1 16.6 - - + +
386R PRO* 1.3 108.8 - - - +
388R TYR* 1.3 62.6 + - - +
390R ALA* 3.6 2.9 + - - +
391R GLU* 3.3 23.8 + - - +
429R GLN* 4.4 4.3 - - - +
81T ARG* 3.2 48.4 + - - +
83T LYS* 4.8 6.9 - - - -
152T VAL* 4.0 17.3 - - + +
158T ILE* 4.2 14.6 - - + +
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Residues in contact with TYR 388 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337R GLU* 3.6 29.3 - - + +
338R MET 2.9 17.5 + - - -
339R LEU* 3.6 2.1 - - - +
384R ALA* 5.2 1.1 - - + -
385R ASN* 3.1 11.7 + - + +
386R PRO 3.1 0.4 - - - -
387R GLU* 1.3 79.1 - - - +
389R ILE* 1.3 65.9 + - - +
391R GLU* 3.2 12.5 + - + +
392R LEU* 3.1 39.0 + - + +
429R GLN* 3.1 61.9 + - + +
430R VAL 4.0 8.1 - - - -
431R ILE* 3.5 26.7 - - + -
462R PHE* 3.2 23.2 - + - -
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Residues in contact with ILE 389 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369R PHE* 5.7 4.3 - - + -
371R LYS* 3.8 34.8 - - + -
384R ALA* 4.0 12.1 - - + +
385R ASN 2.9 21.9 + - - +
386R PRO* 2.9 12.0 + - + +
388R TYR* 1.3 73.4 - - + +
390R ALA* 1.3 67.1 + - - +
392R LEU* 2.9 13.7 + - + +
393R ARG* 2.9 24.0 + - + +
431R ILE* 3.5 23.8 - - + -
115T GLN* 5.1 1.6 - - - +
237T VAL* 3.8 33.7 - - + +
238T SER* 3.8 7.9 - - - -
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Residues in contact with ALA 390 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386R PRO 2.7 15.4 + - - +
387R GLU 3.7 2.9 - - - +
389R ILE* 1.3 72.2 - - - +
391R GLU* 1.3 64.8 + - + +
393R ARG* 2.9 19.2 + - - +
394R ARG* 2.9 14.0 + - - +
152T VAL* 3.3 34.1 - - + -
153T LYS 3.6 13.2 - - - +
154T LYS* 4.1 6.1 - - - +
156T GLY* 5.2 2.0 - - - -
238T SER* 3.6 15.2 - - - +
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Residues in contact with GLU 391 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337R GLU* 5.6 4.5 - - - +
387R GLU 3.3 11.4 + - - +
388R TYR* 3.2 19.1 + - + +
389R ILE 3.1 0.6 - - - -
390R ALA* 1.3 79.0 - - - +
392R LEU* 1.3 63.4 + - + +
394R ARG* 3.0 52.7 + - - +
395R ILE* 2.9 33.3 + - + +
154T LYS 4.5 4.7 - - - +
155T ASP 5.2 4.3 - - - +
156T GLY* 5.5 2.8 - - - -
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Residues in contact with LEU 392 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339R LEU* 4.0 6.3 - - + -
369R PHE* 3.5 27.1 - - + -
388R TYR* 3.4 31.0 - - + +
389R ILE* 2.9 7.7 + - - +
391R GLU* 1.3 76.3 - - + +
393R ARG* 1.3 58.1 + - - +
395R ILE* 3.3 10.6 + - + +
396R LEU* 2.8 38.9 + - + +
431R ILE* 3.5 37.5 - - + -
462R PHE* 3.6 35.4 - - + -
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Residues in contact with ARG 393 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389R ILE* 2.9 20.5 + - + +
390R ALA* 3.0 9.0 - - - +
392R LEU* 1.3 79.8 - - - +
394R ARG* 1.3 60.5 + - - +
396R LEU* 3.1 11.4 + - - +
397R SER* 2.7 24.8 + - - -
403R TRP* 4.3 22.6 + - + +
152T VAL 3.5 4.4 + - - -
154T LYS* 3.9 28.8 - - + +
234T GLU* 2.9 36.0 + - - +
235T ASP* 2.7 43.4 + - - +
237T VAL* 4.6 6.1 - - + -
238T SER* 2.4 50.5 + - - +
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Residues in contact with ARG 394 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390R ALA 2.9 2.5 + - - +
391R GLU* 3.0 43.1 + - - +
393R ARG* 1.3 78.1 - - - +
395R ILE* 1.3 80.1 + - - +
397R SER* 3.0 17.7 + - - -
398R LYS* 3.1 10.1 + - + +
465R ASN* 4.1 19.4 + - - -
154T LYS* 3.7 41.4 - - + +
155T ASP* 5.2 8.6 + - - +
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Residues in contact with ILE 395 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100R LYS* 5.0 7.9 - - - +
391R GLU* 2.9 24.5 + - + +
392R LEU* 3.6 20.2 - - + +
394R ARG* 1.3 89.7 - - - +
396R LEU* 1.3 58.7 + - + +
397R SER 2.7 14.7 + - - -
398R LYS* 3.2 15.5 + - + +
399R GLU* 3.3 16.9 + - + +
461R ALA* 2.8 31.2 - - + +
462R PHE* 4.8 11.4 - - + -
465R ASN* 4.6 18.2 - - - +
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Residues in contact with LEU 396 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339R LEU* 6.5 0.4 - - + -
367R ILE* 4.6 7.2 - - + -
369R PHE* 3.4 39.5 - - + -
392R LEU* 2.8 26.4 + - + +
393R ARG* 3.1 6.3 + - - +
395R ILE* 1.3 72.9 - - + +
397R SER* 1.3 54.9 + - - +
400R SER 2.3 26.4 - - - +
401R VAL* 3.3 25.4 - - + +
403R TRP* 4.2 20.6 + - + -
458R GLY* 3.4 38.6 - - - +
461R ALA* 4.3 8.7 - - + +
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Residues in contact with SER 397 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393R ARG 2.7 16.1 + - - -
394R ARG* 3.0 15.7 - - - -
395R ILE 2.8 0.2 - - - -
396R LEU* 1.3 81.7 - - - +
398R LYS* 1.3 66.5 + - - +
400R SER* 2.9 13.8 + - - +
403R TRP* 5.0 5.0 + - - -
154T LYS* 3.3 26.6 + - - -
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Residues in contact with LYS 398 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394R ARG* 3.1 7.6 + - + +
395R ILE* 3.2 8.5 + - + +
397R SER* 1.3 78.2 - - - +
399R GLU* 1.3 99.7 + - + +
400R SER* 2.8 10.7 + - - -
465R ASN* 6.3 1.3 - - - +
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Residues in contact with GLU 399 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395R ILE* 3.3 10.6 + - + +
398R LYS* 1.3 107.9 + - + +
400R SER* 1.3 70.3 + - - +
401R VAL* 3.5 8.0 + - + +
461R ALA* 3.6 37.2 - - + +
463R LEU* 4.9 10.1 - - + +
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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
------------------------------------------------------------
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