Contacts of the helix formed by residues 449 - 461 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13P TRP* 4.5 2.7 - - + -
25P PHE* 4.0 18.7 - - + +
26P ALA* 3.5 19.5 + - - +
29P ASP* 5.7 0.9 - - - +
30P ARG* 3.0 39.2 - - + +
251P ASP* 2.6 27.5 + - - -
256P ARG* 2.8 30.6 + - - +
257P SER* 3.0 15.4 + - - +
258P MET 3.6 9.9 - - - -
259P VAL* 3.7 14.6 - - + -
447P SER 3.7 1.4 + - - -
448P SER* 1.3 70.1 - - - +
450P ALA* 1.3 62.8 + - - +
452P ILE* 3.1 13.0 + - + +
453P TYR* 2.8 25.5 + - - +
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Residues in contact with ALA 450 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P ALA* 3.6 12.6 - - + -
13P TRP* 3.4 37.0 - - + +
16P TYR* 2.9 32.5 + - + -
25P PHE* 3.9 5.4 - - - -
364P GLY* 4.9 1.1 - - - -
448P SER* 3.1 5.7 + - - +
449P LYS* 1.3 77.4 - - - +
451P ASP* 1.3 58.9 + - - +
453P TYR* 3.3 0.3 + - - +
454P GLU* 2.8 26.8 + - - +
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Residues in contact with ASP 451 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362P TYR 4.2 2.0 - - - +
363P LEU* 3.6 3.8 - - - +
364P GLY* 2.6 34.7 + - - -
365P LYS 3.2 0.6 + - - -
366P GLY 2.8 42.4 + - - +
404P GLN* 5.0 0.4 - - - -
435P VAL* 3.5 21.7 - - + +
436P ALA* 4.7 6.9 - - - +
448P SER* 2.8 20.2 + - - +
450P ALA* 1.3 75.1 - - - +
452P ILE* 1.3 65.9 + - - +
454P GLU* 3.2 5.9 + - - +
455P THR* 2.8 30.6 + - - +
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Residues in contact with ILE 452 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P ASP* 4.1 21.8 - - + -
30P ARG* 5.8 3.8 - - - +
33P ASN* 3.9 23.6 - - + +
259P VAL* 4.2 11.7 - - + -
268P ILE* 3.7 20.9 - - + -
272P THR* 3.7 25.8 - - + +
435P VAL* 4.3 5.8 - - + +
447P SER* 3.9 17.3 - - - +
448P SER 2.9 14.5 + - - +
449P LYS* 3.3 23.1 - - + +
451P ASP* 1.3 74.0 - - - +
453P TYR* 1.3 66.3 + - - +
455P THR* 3.4 6.6 - - - -
456P LYS* 3.1 14.2 + - - +
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Residues in contact with TYR 453 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P LYS* 5.3 0.4 - - - -
16P TYR* 3.0 42.8 - + - -
21P LEU* 3.1 28.3 - - + +
24P VAL* 3.9 27.8 - - + +
25P PHE* 3.3 39.3 - + + -
29P ASP* 3.6 16.1 + - - +
449P LYS 2.8 12.3 + - - +
450P ALA 3.4 7.0 - - - +
452P ILE* 1.3 75.9 - - - +
454P GLU* 1.3 63.0 + - - +
456P LYS* 2.9 19.4 + - + +
457P ASN* 3.0 44.7 + - - -
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Residues in contact with GLU 454 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P ALA* 3.6 10.4 - - - +
15P LYS* 2.8 20.3 + - - -
16P TYR* 2.5 31.1 + - - -
366P GLY* 3.9 12.8 - - - -
367P ILE* 4.3 1.1 - - - +
401P VAL* 3.5 14.1 - - + +
402P ASN* 3.1 56.5 + - + +
450P ALA 2.8 17.9 + - - +
451P ASP* 3.6 3.8 - - - +
453P TYR* 1.3 71.6 - - - +
455P THR* 1.3 52.2 + - - +
457P ASN* 3.1 13.9 + - - +
458P GLY 2.7 31.0 + - - -
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Residues in contact with THR 455 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269P CYS* 5.3 0.2 - - - -
272P THR* 3.6 13.5 - - - +
367P ILE* 3.5 31.9 - - + +
434P GLY 5.1 0.9 - - - -
435P VAL* 3.5 26.5 - - + +
451P ASP 2.8 21.6 + - - -
452P ILE 3.4 4.5 - - - -
454P GLU* 1.3 71.8 - - - +
456P LYS* 1.3 66.0 + - - +
458P GLY* 2.8 11.6 + - - -
459P TYR* 2.8 46.5 + - + +
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Residues in contact with LYS 456 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P ASP* 4.1 18.3 + - - +
32P LYS* 4.7 3.0 - - - +
272P THR* 3.9 30.1 - - + +
275P GLU* 2.7 43.0 + - + +
276P ALA* 4.0 10.3 - - + +
279P GLU* 3.5 31.6 + - - -
452P ILE 3.1 8.2 + - - +
453P TYR* 2.9 13.4 + - + +
455P THR* 1.3 77.8 - - - +
457P ASN* 1.3 66.6 + - - +
459P TYR* 2.8 8.0 + - - +
460P SER* 2.8 31.6 + - - +
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Residues in contact with ASN 457 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P LYS* 5.4 0.8 - - - +
401P VAL* 3.5 17.7 - - + +
453P TYR* 3.0 60.0 + - - +
454P GLU* 3.4 14.6 + - - +
456P LYS* 1.3 83.1 - - - +
458P GLY* 1.3 57.6 + - - +
460P SER* 2.9 9.9 + - - -
461P ALA* 2.8 33.6 + - - +
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Residues in contact with GLY 458 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339P LEU* 4.9 3.5 - - - +
367P ILE* 4.7 7.6 - - - -
396P LEU* 3.4 30.6 - - - +
401P VAL* 3.8 4.4 - - - +
454P GLU 2.7 14.1 + - - -
455P THR 2.8 5.3 + - - -
457P ASN* 1.3 78.8 - - - +
459P TYR* 1.3 65.8 + - - +
461P ALA 3.4 12.5 + - - -
462P PHE* 3.8 4.7 + - - +
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Residues in contact with TYR 459 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P LEU* 4.1 17.3 - - + +
269P CYS* 3.7 9.8 - - - -
272P THR* 3.2 25.1 - - - -
273P SER* 3.3 37.0 - - - -
276P ALA* 3.7 11.7 - - + -
339P LEU* 4.0 23.6 - - + -
341P SER* 2.7 32.3 + - - -
367P ILE* 3.8 19.5 - - + -
433P CYS* 4.3 5.6 - - + -
434P GLY 4.1 2.6 + - - -
455P THR* 2.8 23.7 + - + +
456P LYS* 2.8 7.8 + - - +
458P GLY* 1.3 74.2 - - - +
460P SER* 1.3 55.4 + - - +
462P PHE* 2.7 40.2 + - - +
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Residues in contact with SER 460 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276P ALA* 3.7 21.2 - - - +
279P GLU* 5.6 7.0 - - - -
280P MET* 5.5 5.4 - - - -
456P LYS* 2.8 14.6 + - - +
457P ASN* 2.9 30.7 + - - +
459P TYR* 1.3 72.2 - - - +
461P ALA* 1.3 50.6 + - - +
462P PHE 2.7 10.7 + - - -
463P LEU* 3.0 31.4 + - - +
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Residues in contact with ALA 461 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395P ILE* 2.8 29.1 - - + +
396P LEU* 4.3 12.4 - - + +
399P GLU* 3.6 36.3 - - + +
401P VAL* 4.7 2.0 - - + -
457P ASN 2.8 23.0 + - - +
458P GLY 3.7 7.3 - - - +
459P TYR 3.0 0.4 + - - -
460P SER* 1.3 70.7 + - - +
462P PHE* 1.3 56.9 + - - +
463P LEU* 3.5 7.2 - - - -
464P ASN 3.9 4.0 - - - +
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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