Contacts of the helix formed by residues 449 - 461 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13J TRP* 4.5 2.9 - - + -
25J PHE* 4.0 19.2 - - + +
26J ALA* 3.5 19.6 + - + +
29J ASP* 5.7 0.9 - - + +
30J ARG* 3.0 39.9 - - + +
251J ASP* 2.5 28.3 + - - -
256J ARG* 2.8 30.4 + - - +
257J SER* 3.0 15.2 + - - +
258J MET 3.7 10.5 - - - -
259J VAL* 3.7 14.4 - - + -
447J SER 3.7 1.4 + - - -
448J SER* 1.3 70.1 - - - +
450J ALA* 1.3 64.2 + - - +
452J ILE* 3.1 14.3 + - + +
453J TYR* 2.9 25.3 + - - +
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Residues in contact with ALA 450 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J ALA* 3.6 12.6 - - + -
13J TRP* 3.4 37.3 - - + +
16J TYR* 3.0 33.4 + - + -
25J PHE* 3.9 5.6 - - - -
364J GLY* 4.9 1.8 - - - -
448J SER* 3.1 4.8 + - - +
449J LYS* 1.3 78.9 - - - +
451J ASP* 1.3 57.7 + - - +
453J TYR* 3.3 0.3 + - - +
454J GLU* 2.8 27.4 + - - +
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Residues in contact with ASP 451 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362J TYR 4.2 1.8 - - - +
363J LEU* 3.5 4.3 - - - +
364J GLY* 2.5 34.1 + - - -
366J GLY 2.9 42.4 + - - +
404J GLN* 5.0 0.4 - - - -
435J VAL* 3.5 22.2 - - + +
436J ALA* 4.7 7.1 - - - +
448J SER* 2.7 25.5 + - - +
450J ALA* 1.3 69.9 - - - +
452J ILE* 1.3 67.3 + - - +
454J GLU* 3.2 5.2 + - - +
455J THR* 2.7 30.1 + - - +
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Residues in contact with ILE 452 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ASP* 4.0 23.6 - - + -
30J ARG* 5.8 3.6 - - - +
33J ASN* 3.8 27.4 - - + +
259J VAL* 4.2 12.1 - - + -
268J ILE* 3.6 18.4 - - + -
272J THR* 3.7 25.1 - - + +
435J VAL* 4.2 6.5 - - + +
447J SER* 3.9 17.7 - - - +
448J SER 2.8 20.0 + - - +
449J LYS* 3.3 22.2 - - + +
451J ASP* 1.3 73.2 - - - +
453J TYR* 1.3 64.7 + - - +
455J THR* 3.2 6.6 + - - -
456J LYS* 3.1 17.0 + - - +
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Residues in contact with TYR 453 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LYS* 5.3 0.4 - - - -
16J TYR* 3.1 42.0 - + - -
21J LEU* 3.1 30.0 - - + +
24J VAL* 3.9 22.4 - - + +
25J PHE* 3.3 42.8 - + + -
29J ASP* 3.6 15.9 + - + +
449J LYS 2.9 12.3 + - - +
450J ALA 3.4 7.2 - - - +
452J ILE* 1.3 75.5 - - - +
454J GLU* 1.3 64.7 + - - +
456J LYS* 3.0 17.5 + - + +
457J ASN* 3.1 45.1 + - - +
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Residues in contact with GLU 454 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J ALA* 3.5 10.3 - - + +
15J LYS* 2.8 20.3 + - - -
16J TYR* 2.4 30.8 + - - -
366J GLY* 3.9 12.6 - - - -
367J ILE* 4.8 0.7 - - - -
401J VAL* 3.5 15.1 - - + +
402J ASN* 3.1 58.0 + - + +
450J ALA 2.8 19.0 + - - +
451J ASP* 3.6 3.4 - - - +
453J TYR* 1.3 72.0 - - - +
455J THR* 1.3 57.6 + - - +
457J ASN* 3.2 14.4 + - - +
458J GLY 2.8 24.4 + - - -
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Residues in contact with THR 455 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J CYS* 5.3 0.2 - - - -
272J THR* 3.6 13.7 - - - +
367J ILE* 3.5 31.2 - - + +
434J GLY 5.1 0.7 - - - -
435J VAL* 3.5 26.9 - - + +
451J ASP* 2.7 17.0 + - - +
452J ILE 3.3 9.6 - - - -
454J GLU* 1.3 73.3 - - - +
456J LYS* 1.3 64.8 + - - +
458J GLY* 2.8 11.8 + - - -
459J TYR* 2.9 46.3 + - + +
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Residues in contact with LYS 456 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ASP* 4.1 18.1 + - - +
32J LYS* 4.7 3.8 - - - +
272J THR* 4.0 30.5 - - + +
275J GLU* 2.6 43.4 + - + +
276J ALA* 4.0 10.7 - - + +
279J GLU* 3.6 31.1 + - - -
452J ILE 3.1 7.6 + - - +
453J TYR* 3.0 13.2 + - + +
455J THR* 1.3 77.8 - - - +
457J ASN* 1.3 71.8 + - - +
459J TYR* 2.8 8.4 + - - +
460J SER* 2.8 25.5 + - - +
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Residues in contact with ASN 457 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LYS* 5.4 0.8 - - - +
401J VAL* 3.5 18.4 - - + -
453J TYR* 3.1 60.5 + - - +
454J GLU* 3.5 13.9 + - - +
456J LYS* 1.3 81.7 - - - +
458J GLY* 1.3 57.8 + - - +
460J SER* 2.9 10.4 + - - -
461J ALA* 2.7 33.8 + - - +
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Residues in contact with GLY 458 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339J LEU* 4.9 3.5 - - - +
367J ILE* 4.7 8.3 - - - -
396J LEU* 3.4 31.1 - - - +
401J VAL* 3.8 4.4 - - - +
454J GLU 2.8 14.3 + - - -
455J THR 2.8 5.3 + - - -
457J ASN* 1.3 80.2 - - - +
459J TYR* 1.3 64.8 + - - +
461J ALA 3.5 12.0 + - - -
462J PHE* 3.8 5.2 + - - +
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Residues in contact with TYR 459 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J LEU* 4.1 17.5 - - + +
269J CYS* 3.8 9.4 - - - -
272J THR* 3.2 24.7 - - - -
273J SER* 3.3 38.1 - - - -
276J ALA* 3.6 11.4 - - + -
339J LEU* 4.0 23.3 - - + -
341J SER* 2.7 33.2 + - - -
367J ILE* 3.8 19.5 - - + -
433J CYS* 4.3 6.1 - - + -
434J GLY 4.0 2.4 + - - -
455J THR* 2.9 24.2 + - + +
456J LYS* 2.8 7.9 + - - +
458J GLY* 1.3 74.1 - - - +
460J SER* 1.3 55.6 + - - +
462J PHE* 2.7 39.7 + - - +
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Residues in contact with SER 460 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276J ALA* 3.8 22.6 - - - +
279J GLU* 5.6 6.7 - - - -
280J MET* 5.5 4.5 - - - -
456J LYS* 2.8 14.3 + - - +
457J ASN* 2.9 31.5 + - - +
459J TYR* 1.3 73.5 - - - +
461J ALA* 1.3 56.2 + - - +
462J PHE 2.8 6.4 + - - -
463J LEU* 3.1 30.8 + - - +
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Residues in contact with ALA 461 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395J ILE* 2.9 28.7 - - + +
396J LEU* 4.3 12.5 - - + +
399J GLU* 3.6 36.7 - - + +
401J VAL* 4.7 2.2 - - + -
457J ASN 2.7 23.9 + - - +
458J GLY 3.7 6.8 - - - +
459J TYR 3.0 0.6 + - - -
460J SER* 1.3 69.4 + - - +
462J PHE* 1.3 56.6 + - - +
463J LEU* 3.5 10.8 - - - -
464J ASN 5.7 0.2 - - - -
465J ASN* 4.1 1.1 - - - +
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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