Contacts of the helix formed by residues 385 - 399 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81M ARG* 4.5 13.6 - - - +
83M LYS* 4.3 21.5 - - - +
302M ALA* 5.7 6.5 - - - +
303M THR* 5.4 2.4 + - - +
383Q ASP 4.3 6.5 + - - +
384Q ALA* 1.3 73.9 - - - +
386Q PRO* 1.3 69.8 - - - +
387Q GLU* 3.1 25.1 - - + +
388Q TYR* 3.1 8.0 + - + +
389Q ILE* 3.0 21.8 + - - +
428Q MET 5.2 0.8 + - - -
429Q GLN* 2.7 33.8 + - - +
430Q VAL 4.7 1.4 + - - -
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Residues in contact with PRO 386 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83M LYS* 5.1 2.7 - - - +
150M VAL* 4.9 6.3 - - + -
152M VAL* 3.9 12.1 - - + -
238M SER* 3.5 26.7 - - - +
239M ALA 3.9 9.9 - - - +
240M GLU* 3.7 33.2 - - + +
371Q LYS* 4.8 1.1 - - - -
384Q ALA 3.8 3.5 - - - +
385Q ASN* 1.3 78.5 - - + +
387Q GLU* 1.3 81.7 + - - +
389Q ILE* 2.9 13.5 + - + +
390Q ALA* 2.7 36.0 + - - +
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Residues in contact with GLU 387 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81M ARG* 3.2 48.4 + - - +
83M LYS* 4.9 6.4 - - - -
150M VAL* 5.9 1.4 - - - +
152M VAL* 4.0 17.9 - - + +
158M ILE* 4.3 15.2 - - + +
385Q ASN* 3.1 16.8 - - + +
386Q PRO* 1.3 107.7 - - - +
388Q TYR* 1.3 63.2 + - - +
390Q ALA* 3.6 3.5 + - - +
391Q GLU* 3.3 23.7 + - - +
429Q GLN* 4.5 4.7 - - - +
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Residues in contact with TYR 388 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337Q GLU* 3.6 29.8 - - + +
338Q MET 2.9 18.0 + - - -
339Q LEU* 3.7 1.9 - - - +
384Q ALA* 5.2 1.1 - - + -
385Q ASN* 3.1 11.8 + - + +
386Q PRO 3.1 0.4 - - - -
387Q GLU* 1.3 79.0 - - - +
389Q ILE* 1.3 67.4 + - - +
391Q GLU* 3.1 12.2 + - + +
392Q LEU* 3.1 40.6 + - + +
429Q GLN* 3.1 61.9 + - + +
430Q VAL 4.0 8.1 - - - -
431Q ILE* 3.5 27.1 - - + -
462Q PHE* 3.2 22.7 - + - -
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Residues in contact with ILE 389 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M GLN* 5.0 1.1 - - - +
237M VAL* 3.8 34.8 - - + +
238M SER* 3.9 7.2 - - - -
369Q PHE* 5.7 3.6 - - + -
371Q LYS* 3.8 35.4 - - + -
384Q ALA* 3.9 13.2 - - + +
385Q ASN 3.0 21.6 + - - +
386Q PRO* 2.9 10.6 + - + +
388Q TYR* 1.3 73.4 - - + +
390Q ALA* 1.3 67.9 + - - +
392Q LEU* 3.0 14.1 + - + +
393Q ARG* 2.9 23.8 + - + +
431Q ILE* 3.5 24.5 - - + -
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Residues in contact with ALA 390 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152M VAL* 3.4 33.2 - - + -
153M LYS 3.6 13.5 - - - +
154M LYS* 4.1 6.7 - - - +
156M GLY* 5.3 2.2 - - - -
238M SER* 3.6 15.2 - - - +
386Q PRO 2.7 14.0 + - - +
387Q GLU 3.7 3.6 - - - +
389Q ILE* 1.3 73.1 - - - +
391Q GLU* 1.3 65.5 + - - +
393Q ARG* 3.0 10.9 + - - +
394Q ARG* 3.0 22.2 + - - +
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Residues in contact with GLU 391 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154M LYS 4.5 4.7 - - - +
155M ASP 5.3 4.0 - - - +
156M GLY* 5.6 2.8 - - - -
337Q GLU* 5.6 4.3 - - - +
387Q GLU 3.3 12.7 + - - +
388Q TYR* 3.1 18.5 + - + +
389Q ILE 3.1 0.4 - - - -
390Q ALA* 1.3 79.7 - - - +
392Q LEU* 1.3 64.3 + - + +
394Q ARG* 3.1 52.0 + - - +
395Q ILE* 2.9 33.2 + - + +
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Residues in contact with LEU 392 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339Q LEU* 4.0 9.0 - - + -
369Q PHE* 3.6 26.2 - - + -
388Q TYR* 3.5 30.1 - - + +
389Q ILE* 3.0 7.5 + - - +
391Q GLU* 1.3 76.4 - - + +
393Q ARG* 1.3 58.0 + - - +
395Q ILE* 3.6 9.8 - - + +
396Q LEU* 2.8 39.4 + - + +
431Q ILE* 3.5 38.1 - - + -
462Q PHE* 3.6 36.3 - - + -
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Residues in contact with ARG 393 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152M VAL 3.6 3.6 + - - -
154M LYS* 3.9 29.9 - - + +
234M GLU* 2.7 44.0 + - - +
235M ASP* 2.8 40.4 + - - +
237M VAL* 4.6 8.5 - - + -
238M SER* 2.5 48.0 + - - +
389Q ILE* 2.9 20.8 + - + +
390Q ALA* 3.0 9.2 - - - +
392Q LEU* 1.3 80.0 - - - +
394Q ARG* 1.3 66.0 + - - +
396Q LEU* 3.0 11.9 + - - +
397Q SER* 2.8 19.0 + - - -
403Q TRP* 4.3 20.3 + - + +
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Residues in contact with ARG 394 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154M LYS* 3.8 39.4 - - + +
155M ASP* 5.3 8.1 + - - +
390Q ALA 3.0 3.2 + - - +
391Q GLU* 3.1 43.6 + - - +
393Q ARG* 1.3 77.8 - - - +
395Q ILE* 1.3 72.2 + - - +
397Q SER* 3.0 19.5 + - - -
398Q LYS* 3.1 9.6 + - + +
465Q ASN* 3.3 34.3 + - - +
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Residues in contact with ILE 395 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Q LYS* 5.0 4.9 - - - +
391Q GLU* 2.9 25.4 + - + +
392Q LEU* 3.6 20.2 - - + +
394Q ARG* 1.3 81.1 - - - +
396Q LEU* 1.3 57.5 + - + +
397Q SER 2.7 15.0 + - - -
398Q LYS* 3.2 15.4 + - + +
399Q GLU* 3.3 16.6 + - + +
461Q ALA* 2.8 31.0 - - + +
462Q PHE* 4.7 10.3 - - + -
464Q ASN 4.4 5.4 - - - +
465Q ASN* 3.4 32.1 - - - +
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Residues in contact with LEU 396 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339Q LEU* 6.5 0.4 - - + -
367Q ILE* 4.6 7.0 - - + -
369Q PHE* 3.4 39.7 - - + -
392Q LEU* 2.8 28.0 + - + +
393Q ARG* 3.0 5.8 + - - +
395Q ILE* 1.3 72.4 - - + +
397Q SER* 1.3 55.2 + - - +
400Q SER 2.3 27.0 - - - +
401Q VAL* 3.3 24.9 - - + +
403Q TRP* 4.2 21.4 + - + -
458Q GLY* 3.4 39.5 - - - +
461Q ALA* 4.3 8.7 - - + +
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Residues in contact with SER 397 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154M LYS* 3.3 26.7 + - - -
393Q ARG* 2.8 15.6 + - - -
394Q ARG* 3.0 13.0 - - - -
395Q ILE 2.7 3.4 + - - -
396Q LEU* 1.3 80.8 + - - +
398Q LYS* 1.3 68.2 + - - +
400Q SER* 2.9 14.0 + - - +
403Q TRP* 5.0 5.2 + - - -
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Residues in contact with LYS 398 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394Q ARG* 3.1 7.8 + - + +
395Q ILE* 3.8 9.0 - - + +
397Q SER* 1.3 81.8 - - - +
399Q GLU* 1.3 98.8 + - + +
400Q SER* 2.8 7.3 + - - -
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Residues in contact with GLU 399 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395Q ILE* 3.3 9.2 + - + +
398Q LYS* 1.3 108.6 + - + +
400Q SER* 1.3 71.7 + - - +
401Q VAL* 3.5 8.0 + - + +
461Q ALA* 3.6 36.7 - - + +
463Q 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
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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