Contacts of the helix formed by residues 449 - 461 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13U TRP* 4.5 2.7 - - + -
25U PHE* 4.0 18.9 - - + +
26U ALA* 3.5 19.9 + - - +
29U ASP* 5.8 0.9 - - + +
30U ARG* 3.0 40.3 - - + +
251U ASP* 2.6 28.6 + - - -
256U ARG* 2.8 30.2 + - - +
257U SER* 3.0 16.4 + - - +
258U MET 3.7 9.9 - - - -
259U VAL* 3.7 14.6 - - + -
447U SER 3.7 1.2 + - - -
448U SER* 1.3 70.8 - - - +
450U ALA* 1.3 64.0 - - - +
452U ILE* 3.1 14.1 + - + +
453U TYR* 2.9 24.8 + - - +
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Residues in contact with ALA 450 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12U ALA* 3.6 11.4 - - + -
13U TRP* 3.4 37.7 - - + +
16U TYR* 2.9 32.8 + - + -
25U PHE* 3.9 5.1 - - - -
364U GLY* 4.9 1.6 - - - -
448U SER* 3.1 4.8 + - - +
449U LYS* 1.3 79.9 - - - +
451U ASP* 1.3 57.1 + - - +
453U TYR* 3.3 0.6 + - - -
454U GLU* 2.8 27.0 + - - +
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Residues in contact with ASP 451 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362U TYR 4.2 1.6 - - - +
363U LEU* 3.5 4.0 - - - +
364U GLY* 2.5 34.3 + - - -
365U LYS 3.2 0.4 + - - -
366U GLY 2.8 42.0 + - - +
404U GLN* 5.0 0.2 - - - -
435U VAL* 3.5 21.6 - - + +
436U ALA* 4.7 7.6 - - - +
448U SER* 2.8 25.6 + - - +
450U ALA* 1.3 70.5 - - - +
452U ILE* 1.3 66.0 + - - +
454U GLU* 3.2 5.7 + - - +
455U THR* 2.7 30.1 + - - +
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Residues in contact with ILE 452 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U ASP* 4.1 23.1 - - + -
30U ARG* 5.8 3.4 - - - +
33U ASN* 3.8 27.1 - - + +
259U VAL* 4.2 12.1 - - + -
268U ILE* 3.7 18.2 - - + -
272U THR* 3.7 24.9 - - + +
435U VAL* 4.2 6.9 - - + +
447U SER* 4.0 17.0 - - - +
448U SER 2.8 15.0 + - - +
449U LYS* 3.3 22.4 - - + +
451U ASP* 1.3 75.4 - - - +
453U TYR* 1.3 61.9 - - - +
455U THR* 3.2 7.0 + - - -
456U LYS* 3.1 17.0 + - - +
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Residues in contact with TYR 453 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U LYS* 5.3 0.2 - - - -
16U TYR* 3.1 42.8 - + - -
21U LEU* 3.1 28.9 - - + +
24U VAL* 4.0 22.1 - - + +
25U PHE* 3.4 43.5 - + + -
29U ASP* 3.6 15.6 + - - +
449U LYS 2.9 11.6 + - - +
450U ALA 3.4 6.5 - - - +
452U ILE* 1.3 73.4 - - - +
454U GLU* 1.3 66.4 + - - +
456U LYS* 2.9 17.9 + - + +
457U ASN* 3.1 45.3 + - - -
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Residues in contact with GLU 454 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12U ALA* 3.6 10.2 - - - +
15U LYS* 2.8 19.8 + - - -
16U TYR* 2.4 31.1 + - - -
366U GLY* 3.9 13.0 - - - -
367U ILE* 4.4 0.7 - - - +
401U VAL* 3.4 14.7 - - + +
402U ASN* 3.1 57.8 + - + +
450U ALA 2.8 17.9 + - - +
451U ASP 3.6 3.1 - - - +
453U TYR* 1.3 71.0 - - - +
455U THR* 1.3 52.1 + - - +
457U ASN* 3.1 13.9 + - - +
458U GLY 2.8 30.7 + - - -
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Residues in contact with THR 455 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272U THR* 3.6 13.0 - - - +
367U ILE* 3.5 31.6 - - + +
434U GLY 5.1 0.7 - - - -
435U VAL* 3.5 26.8 - - + +
451U ASP 2.7 18.5 + - - -
452U ILE 3.3 9.2 - - - -
454U GLU* 1.3 72.2 - - - +
456U LYS* 1.3 65.3 + - - +
458U GLY* 2.9 3.3 + - - -
459U TYR* 2.9 54.6 + - + +
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Residues in contact with LYS 456 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U ASP* 4.1 18.5 + - - +
32U LYS* 4.7 3.6 - - - +
272U THR* 3.9 30.9 - - + +
275U GLU* 2.6 43.5 + - + +
276U ALA* 4.0 10.5 - - + +
279U GLU* 3.6 30.9 + - - -
452U ILE 3.1 7.3 + - - +
453U TYR* 2.9 13.1 + - + +
455U THR* 1.3 78.4 - - - +
457U ASN* 1.3 70.8 + - - +
459U TYR* 2.8 9.0 + - - +
460U SER* 2.8 25.9 + - - +
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Residues in contact with ASN 457 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U LYS* 5.4 0.6 - - - +
401U VAL* 3.5 16.8 - - + +
453U TYR* 3.1 60.3 + - - +
454U GLU* 3.5 13.9 + - - +
456U LYS* 1.3 82.3 - - - +
458U GLY* 1.3 54.6 + - - +
460U SER* 2.9 11.2 + - - +
461U ALA* 2.7 37.6 + - - +
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Residues in contact with GLY 458 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339U LEU* 4.9 4.1 - - - +
367U ILE* 4.7 8.1 - - - -
396U LEU* 3.4 31.1 - - - +
401U VAL* 3.8 4.4 - - - +
454U GLU 2.8 13.8 + - - -
455U THR 2.9 5.5 + - - -
457U ASN* 1.3 78.6 - - - +
459U TYR* 1.3 65.0 + - - +
461U ALA 3.5 12.3 + - - -
462U PHE* 3.8 4.9 + - - +
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Residues in contact with TYR 459 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U LEU* 4.1 17.7 - - + +
269U CYS* 3.7 9.8 - - - -
272U THR* 3.1 25.4 - - - -
273U SER* 3.3 37.9 - - - -
276U ALA* 3.7 11.7 - - + -
339U LEU* 4.0 24.2 - - + -
341U SER* 2.8 33.3 + - - -
367U ILE* 3.8 19.1 - - + -
433U CYS* 4.3 5.6 - - + -
434U GLY 4.1 2.3 + - - -
455U THR* 2.9 24.2 + - + +
456U LYS* 2.8 7.2 + - - +
458U GLY* 1.3 74.3 - - - +
460U SER* 1.3 56.5 + - - +
462U PHE* 2.7 39.9 + - - +
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Residues in contact with SER 460 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276U ALA* 3.7 22.3 - - - +
279U GLU* 5.6 7.0 - - - -
280U MET* 5.5 4.9 - - - -
456U LYS* 2.8 15.8 + - - +
457U ASN* 2.9 31.2 + - - +
459U TYR* 1.3 73.6 - - - +
461U ALA* 1.3 54.4 + - - +
462U PHE 2.8 6.6 + - - -
463U LEU* 3.1 31.2 + - - +
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Residues in contact with ALA 461 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395U ILE* 2.8 28.9 - - + +
396U LEU* 4.3 12.4 - - + +
399U GLU* 3.6 36.2 - - + +
401U VAL* 4.7 2.5 - - + -
457U ASN 2.7 23.1 + - - +
458U GLY 3.7 7.3 - - - +
459U TYR 3.0 0.4 + - - -
460U SER* 1.3 70.3 + - - +
462U PHE* 1.3 56.8 + - - +
463U LEU* 3.5 9.0 - - - -
464U ASN 5.1 1.1 + - - +
465U ASN* 4.8 0.2 - - - +
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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