Contacts of the helix formed by residues 449 - 461 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C TRP* 4.5 2.7 - - + -
25C PHE* 3.9 18.4 - - + +
26C ALA* 3.5 19.7 + - + +
29C ASP* 5.7 0.9 - - - +
30C ARG* 3.0 39.9 - - + +
251C ASP* 2.6 27.9 + - - -
256C ARG* 2.8 29.6 + - - +
257C SER* 3.0 15.8 + - - +
258C MET 3.6 10.8 - - - -
259C VAL* 3.7 14.6 - - + -
447C SER 3.7 1.0 + - - -
448C SER* 1.3 70.3 - - - +
450C ALA* 1.3 63.8 + - - +
452C ILE* 3.1 14.0 + - + +
453C TYR* 2.9 24.9 + - - +
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Residues in contact with ALA 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 3.6 12.8 - - + -
13C TRP* 3.4 37.5 - - + +
16C TYR* 2.9 32.6 + - + -
25C PHE* 3.9 5.1 - - - -
364C GLY* 4.9 1.1 - - - -
448C SER* 3.1 5.2 + - - +
449C LYS* 1.3 80.5 - - - +
451C ASP* 1.3 57.3 + - - +
453C TYR* 3.3 0.7 + - - +
454C GLU* 2.8 27.7 + - - +
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Residues in contact with ASP 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C TYR 4.1 2.1 - - - +
363C LEU* 3.5 4.3 - - - +
364C GLY* 2.5 35.2 + - - -
365C LYS 3.2 0.4 + - - -
366C GLY 2.8 41.5 + - - +
404C GLN* 5.0 0.7 - - - -
435C VAL* 3.5 21.6 - - + +
436C ALA* 4.7 6.9 - - - +
448C SER* 2.8 25.0 + - - +
450C ALA* 1.3 71.3 - - - +
452C ILE* 1.3 66.1 + - - +
454C GLU* 3.2 5.5 + - - +
455C THR* 2.8 29.8 + - - -
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Residues in contact with ILE 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 4.1 22.4 - - + -
30C ARG* 5.8 3.4 - - - +
33C ASN* 3.9 27.8 - - + +
259C VAL* 4.2 11.7 - - + -
268C ILE* 3.7 17.9 - - + -
272C THR* 3.7 26.0 - - + +
435C VAL* 4.3 5.6 - - + +
447C SER* 3.9 16.8 - - - +
448C SER 2.8 16.8 + - - +
449C LYS* 3.1 23.1 + - + +
451C ASP* 1.3 77.4 - - - +
453C TYR* 1.3 63.9 + - - +
455C THR* 3.3 6.5 + - - -
456C LYS* 3.1 17.8 + - - +
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Residues in contact with TYR 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LYS* 5.3 0.7 - - - -
16C TYR* 3.0 43.7 - + - -
21C LEU* 3.1 28.9 - - + +
24C VAL* 4.0 22.2 - - + +
25C PHE* 3.3 41.7 - + + -
29C ASP* 3.6 15.4 + - - +
449C LYS 2.9 12.2 + - - +
450C ALA 3.4 6.7 - - - +
452C ILE* 1.3 75.9 - - - +
454C GLU* 1.3 63.4 + - - +
456C LYS* 2.9 18.8 + - + +
457C ASN* 3.0 45.1 + - - -
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Residues in contact with GLU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 3.6 10.2 - - - +
15C LYS* 2.8 20.3 + - - -
16C TYR* 2.4 31.3 + - - -
366C GLY* 3.9 12.8 - - - -
367C ILE* 4.9 0.4 - - - -
401C VAL* 3.5 13.5 - - + +
402C ASN* 3.1 57.5 + - + +
450C ALA 2.8 17.7 + - - +
451C ASP* 3.6 3.4 - - - +
453C TYR* 1.3 72.4 - - - +
455C THR* 1.3 51.8 + - - +
457C ASN* 3.1 14.1 + - - +
458C GLY 2.8 31.2 + - - -
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Residues in contact with THR 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C THR* 3.6 13.0 - - - +
366C GLY 5.1 0.2 + - - -
367C ILE* 3.6 31.4 - - + +
434C GLY 5.1 1.3 - - - -
435C VAL* 3.5 26.9 - - + +
451C ASP 2.8 22.9 + - - -
452C ILE 3.4 4.3 - - - -
454C GLU* 1.3 71.7 - - - +
456C LYS* 1.3 64.6 + - - +
458C GLY* 2.9 3.8 + - - -
459C TYR* 2.9 54.4 + - + +
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Residues in contact with LYS 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 4.1 17.2 + - - +
32C LYS* 4.8 3.4 - - - +
272C THR* 3.9 30.3 - - + +
275C GLU* 2.7 44.3 + - + +
276C ALA* 4.0 10.8 - - + +
279C GLU* 3.5 31.3 + - - -
452C ILE 3.1 8.2 + - - +
453C TYR* 2.9 13.0 + - + +
455C THR* 1.3 77.8 - - - +
457C ASN* 1.3 70.6 + - - +
459C TYR* 2.8 9.5 + - - +
460C SER* 2.8 25.1 + - - +
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Residues in contact with ASN 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LYS* 5.4 0.8 - - - +
401C VAL* 3.5 17.5 - - + +
453C TYR* 3.0 59.5 + - - +
454C GLU* 3.4 15.0 + - - +
456C LYS* 1.3 82.6 - - - +
458C GLY* 1.3 57.9 - - - +
460C SER* 2.9 11.2 + - - -
461C ALA* 2.8 33.6 + - - +
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Residues in contact with GLY 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C LEU* 4.9 2.9 - - - +
367C ILE* 4.7 8.1 - - - -
396C LEU* 3.4 30.5 - - - +
401C VAL* 3.8 4.5 - - - +
454C GLU 2.8 14.8 + - - -
455C THR 2.9 5.6 + - - -
457C ASN* 1.3 80.2 - - - +
459C TYR* 1.3 64.4 + - - +
461C ALA 3.5 12.1 + - - +
462C PHE* 3.8 5.2 + - - +
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Residues in contact with TYR 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 4.1 17.9 - - + +
269C CYS* 3.8 9.6 - - - +
272C THR* 3.2 24.7 - - - -
273C SER* 3.3 37.9 - - - -
276C ALA* 3.7 11.0 - - + -
339C LEU* 4.0 23.1 - - + -
341C SER* 2.7 33.3 + - - -
367C ILE* 3.8 12.8 - - + -
433C CYS* 4.3 6.5 - - + -
434C GLY 4.1 2.6 + - - -
455C THR* 2.9 30.3 + - + +
456C LYS* 2.8 7.6 + - - +
458C GLY* 1.3 73.8 - - - +
460C SER* 1.3 56.0 + - - +
462C PHE* 2.7 39.5 + - - +
463C LEU 4.1 0.2 + - - -
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Residues in contact with SER 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C ALA* 3.8 21.6 - - - +
279C GLU* 5.6 6.7 - - - -
280C MET* 5.5 4.9 - - - -
456C LYS* 2.8 13.8 + - - +
457C ASN* 2.9 31.5 + - - -
459C TYR* 1.3 73.3 - - - +
461C ALA* 1.3 53.0 + - - +
462C PHE 2.7 10.4 + - - -
463C LEU* 3.1 30.7 + - - +
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Residues in contact with ALA 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395C ILE* 2.8 29.7 - - + +
396C LEU* 4.3 11.9 - - + +
399C GLU* 3.6 36.7 - - + +
401C VAL* 4.6 2.0 - - + -
457C ASN 2.8 23.3 + - - +
458C GLY 3.7 7.7 - - - +
459C TYR 3.1 0.4 - - - -
460C SER* 1.3 69.6 + - - +
462C PHE* 1.3 56.9 + - - +
463C LEU* 3.5 11.4 - - - -
464C ASN 4.5 1.4 - - - +
465C ASN* 5.8 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