Contacts of the helix formed by residues 449 - 461 (chain S) 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 LYS 449 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13S TRP* 4.5 2.7 - - + -
25S PHE* 3.9 18.8 - - + +
26S ALA* 3.5 18.9 + - + +
29S ASP* 5.7 0.9 - - + +
30S ARG* 3.0 40.5 - - + +
251S ASP* 2.6 27.7 + - - -
256S ARG* 2.8 30.8 + - - +
257S SER* 3.0 16.2 + - - +
258S MET 3.7 10.3 - - - -
259S VAL* 3.7 14.4 - - + -
447S SER 3.7 1.2 + - - -
448S SER* 1.3 70.2 - - - +
450S ALA* 1.3 64.8 + - - +
452S ILE* 3.1 14.4 + - + +
453S TYR* 2.9 25.3 + - - +
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Residues in contact with ALA 450 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S ALA* 3.6 12.6 - - + -
13S TRP* 3.4 38.1 - - + +
16S TYR* 2.9 32.5 + - + -
25S PHE* 3.9 5.1 - - - -
364S GLY* 4.9 1.3 - - - -
448S SER* 3.4 5.3 + - - +
449S LYS* 1.3 79.6 - - - +
451S ASP* 1.3 57.9 + - - +
453S TYR* 3.4 0.2 - - - +
454S GLU* 2.8 27.1 + - - +
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Residues in contact with ASP 451 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362S TYR 4.2 1.4 - - - +
363S LEU* 3.5 3.6 - - - +
364S GLY* 2.5 36.2 + - - -
365S LYS 4.2 0.2 - - - -
366S GLY 2.8 41.9 + - - +
404S GLN* 5.0 0.4 - - - -
435S VAL* 3.5 21.1 - - + +
436S ALA* 4.7 7.6 - - - +
448S SER* 2.8 20.5 + - - +
450S ALA* 1.3 74.5 - - - +
452S ILE* 1.3 67.4 + - - +
454S GLU* 3.2 5.3 + - - -
455S THR* 2.8 29.8 + - - +
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Residues in contact with ILE 452 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S ASP* 4.1 22.4 - - + -
30S ARG* 5.8 3.6 - - - +
33S ASN* 3.9 23.8 - - + +
259S VAL* 4.2 12.3 - - + -
268S ILE* 3.7 21.5 - - + -
272S THR* 3.7 25.3 - - + +
435S VAL* 4.3 6.0 - - + +
447S SER* 3.9 16.8 - - - +
448S SER 2.8 15.0 + - - +
449S LYS* 3.3 22.7 - - + +
451S ASP* 1.3 73.5 - - - +
453S TYR* 1.3 67.9 + - - +
455S THR* 3.2 6.4 + - - -
456S LYS* 3.1 14.7 + - - +
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Residues in contact with TYR 453 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S LYS* 5.3 0.2 - - - -
16S TYR* 3.0 43.5 - + - +
21S LEU* 3.1 28.3 - - + +
24S VAL* 4.0 23.0 - - + +
25S PHE* 3.4 41.1 - + + -
29S ASP* 3.6 15.4 + - + +
449S LYS 2.9 12.0 + - - +
450S ALA 3.4 6.7 - - - +
452S ILE* 1.3 76.5 - - - +
454S GLU* 1.3 64.5 + - - +
456S LYS* 2.9 18.4 + - + +
457S ASN* 3.1 44.2 + - - -
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Residues in contact with GLU 454 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S ALA* 3.5 11.3 - - + +
15S LYS* 2.8 20.7 + - - -
16S TYR* 2.6 30.0 + - - -
366S GLY* 3.9 13.2 - - - -
367S ILE* 4.4 0.9 - - - +
401S VAL* 3.4 14.8 - - + +
402S ASN* 3.0 56.9 + - + +
450S ALA 2.8 17.5 + - - +
451S ASP 3.6 3.6 - - - +
453S TYR* 1.3 73.0 - - - +
455S THR* 1.3 58.4 + - - +
457S ASN* 3.1 15.0 + - - +
458S GLY 2.8 24.6 + - - -
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Residues in contact with THR 455 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269S CYS* 5.2 0.2 - - - -
272S THR* 3.6 13.0 - - - +
367S ILE* 3.4 31.9 - - + +
434S GLY 5.1 0.9 - - - -
435S VAL* 3.6 26.5 - - + +
451S ASP 2.8 22.4 + - - -
452S ILE 3.4 4.7 - - - -
454S GLU* 1.3 72.0 - - - +
456S LYS* 1.3 65.2 + - - +
458S GLY* 2.9 3.8 + - - -
459S TYR* 2.8 54.3 + - + +
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Residues in contact with LYS 456 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S ASP* 4.1 17.6 + - - +
32S LYS* 4.7 3.6 - - - +
272S THR* 4.0 30.7 - - + +
275S GLU* 2.6 43.4 + - + +
276S ALA* 4.0 9.9 - - + +
279S GLU* 3.5 30.8 + - - -
452S ILE 3.1 7.4 + - - +
453S TYR* 2.9 13.5 + - + +
455S THR* 1.3 79.3 - - - +
457S ASN* 1.3 66.3 + - - +
459S TYR* 2.8 9.5 + - - +
460S SER* 2.8 30.5 + - - +
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Residues in contact with ASN 457 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S LYS* 5.4 1.2 - - - +
401S VAL* 3.5 17.7 - - + +
453S TYR* 3.1 61.0 + - - +
454S GLU* 3.4 14.0 + - - +
456S LYS* 1.3 82.7 - - - +
458S GLY* 1.3 54.5 + - - +
460S SER* 2.8 10.7 + - - -
461S ALA* 2.7 38.5 + - - +
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Residues in contact with GLY 458 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339S LEU* 4.8 3.7 - - - +
367S ILE* 4.7 8.1 - - - -
396S LEU* 3.4 30.8 - - - +
401S VAL* 3.8 4.0 - - - +
454S GLU 2.8 14.2 + - - -
455S THR 2.9 5.8 + - - -
457S ASN* 1.3 78.4 - - - +
459S TYR* 1.3 65.7 + - - +
461S ALA 3.5 12.0 + - - -
462S PHE* 3.8 5.5 + - - +
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Residues in contact with TYR 459 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102S LEU* 4.1 17.0 - - + +
269S CYS* 3.6 12.8 - - - -
272S THR* 3.2 24.9 - - - -
273S SER* 3.3 37.9 - - - -
276S ALA* 3.7 11.0 - - + -
339S LEU* 4.0 24.9 - - + -
341S SER* 2.7 33.8 + - - -
367S ILE* 3.8 19.5 - - + -
433S CYS* 4.3 5.8 - - + -
434S GLY 4.0 2.4 + - - -
455S THR* 2.8 20.1 + - + +
456S LYS 2.8 7.2 + - - +
458S GLY* 1.3 74.8 - - - +
460S SER* 1.3 56.5 + - - +
462S PHE* 2.7 39.4 + - - +
463S LEU 4.1 0.2 + - - -
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Residues in contact with SER 460 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276S ALA* 3.8 21.9 - - - +
279S GLU* 5.6 7.0 - - - -
280S MET* 5.6 4.7 - - - -
456S LYS* 2.8 14.5 + - - +
457S ASN* 2.8 34.5 + - - +
459S TYR* 1.3 73.5 - - - +
461S ALA* 1.3 51.4 + - - +
462S PHE 2.7 11.1 + - - -
463S LEU* 3.0 31.8 + - - +
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Residues in contact with ALA 461 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395S ILE* 2.9 29.3 - - + +
396S LEU* 4.3 12.1 - - + +
399S GLU* 3.6 36.1 - - + +
401S VAL* 4.7 2.0 - - + -
457S ASN 2.7 23.7 + - - +
458S GLY 3.7 7.5 - - - +
459S TYR 3.1 0.4 + - - -
460S SER* 1.3 70.2 + - - +
462S PHE* 1.3 57.0 + - - +
463S LEU* 3.5 10.5 - - - -
464S ASN 5.2 0.7 - - - +
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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