Contacts of the helix formed by residues 449 - 461 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13K TRP* 4.5 3.1 - - + -
25K PHE* 3.9 18.0 - - + -
26K ALA* 3.5 19.7 + - - +
29K ASP* 5.7 1.1 - - - +
30K ARG* 3.0 39.7 - - + +
251K ASP* 2.6 28.4 + - - -
256K ARG* 2.8 31.2 + - - +
257K SER* 3.0 15.3 + - - +
258K MET 3.7 9.9 - - - -
259K VAL* 3.7 14.4 - - + -
447K SER 3.7 1.4 + - - -
448K SER* 1.3 69.5 - - - +
450K ALA* 1.3 63.8 + - - +
452K ILE* 3.1 14.7 + - + +
453K TYR* 2.9 24.9 + - - +
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Residues in contact with ALA 450 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ALA* 3.6 12.3 - - + -
13K TRP* 3.4 37.5 - - + +
16K TYR* 2.9 32.9 + - + -
25K PHE* 4.0 4.9 - - - -
364K GLY 4.9 1.1 - - - +
448K SER* 3.1 4.8 + - - +
449K LYS* 1.3 78.5 - - - +
451K ASP* 1.3 58.9 + - - +
453K TYR* 3.3 0.9 + - - +
454K GLU* 2.8 26.5 + - - +
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Residues in contact with ASP 451 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362K TYR 4.2 2.0 - - - +
363K LEU* 3.6 4.0 - - - +
364K GLY* 2.5 34.7 + - - -
365K LYS 3.2 0.2 + - - -
366K GLY 2.8 42.4 + - - +
404K GLN* 5.0 0.4 - - - -
435K VAL* 3.5 21.9 - - + +
436K ALA* 4.7 6.7 - - - +
448K SER* 2.8 20.1 + - - +
450K ALA* 1.3 75.3 - - - +
452K ILE* 1.3 66.3 + - - +
454K GLU* 3.6 5.3 - - - +
455K THR* 2.7 30.5 + - - +
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Residues in contact with ILE 452 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K ASP* 4.1 22.9 - - + +
30K ARG* 5.7 2.9 - - - +
33K ASN* 3.9 24.0 - - + +
259K VAL* 4.2 12.6 - - + -
268K ILE* 3.7 21.1 - - + -
272K THR* 3.6 25.9 - - + +
435K VAL* 4.3 6.0 - - + +
447K SER* 4.0 16.6 - - - +
448K SER 2.9 13.5 + - - +
449K LYS* 3.3 23.1 - - + +
451K ASP* 1.3 76.1 - - - +
453K TYR* 1.3 67.1 + - - +
455K THR* 3.3 6.2 + - - -
456K LYS* 3.1 15.2 + - - +
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Residues in contact with TYR 453 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LYS* 5.3 0.7 - - - -
16K TYR* 3.0 43.5 - + - -
21K LEU* 3.1 28.9 - - + +
24K VAL* 4.0 28.0 - - + +
25K PHE* 3.4 37.0 - + + -
29K ASP* 3.7 16.3 + - + +
449K LYS 2.9 12.4 + - - +
450K ALA 3.4 7.0 - - - +
452K ILE* 1.3 73.2 - - - +
454K GLU* 1.3 66.0 + - - +
456K LYS* 2.9 19.1 + - + +
457K ASN* 3.1 43.4 + - - -
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Residues in contact with GLU 454 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ALA* 3.5 10.7 - - - +
15K LYS* 2.8 20.2 + - - -
16K TYR* 2.5 31.8 + - - -
366K GLY* 3.9 12.1 - - - -
367K ILE* 4.4 1.1 - - - +
401K VAL* 3.5 15.1 - - + +
402K ASN* 3.1 57.0 + - + +
450K ALA 2.8 19.2 + - - +
451K ASP 3.6 3.4 - - - +
453K TYR* 1.3 71.3 - - - +
455K THR* 1.3 57.4 + - - +
457K ASN* 3.1 14.5 + - - +
458K GLY 2.8 23.9 + - - -
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Residues in contact with THR 455 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K CYS* 5.3 0.2 - - - -
272K THR* 3.6 8.7 - - - +
367K ILE* 3.5 32.3 - - + +
434K GLY 5.1 0.9 - - - -
435K VAL* 3.5 26.8 - - + +
451K ASP 2.7 22.8 + - - -
452K ILE 3.4 5.2 - - - -
454K GLU* 1.3 72.4 - - - +
456K LYS* 1.3 66.2 + - - +
458K GLY* 2.9 3.5 + - - -
459K TYR* 2.9 57.5 + - + +
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Residues in contact with LYS 456 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K ASP* 4.0 19.1 + - - +
32K LYS* 4.7 3.6 - - - +
272K THR* 3.9 31.0 - - + +
275K GLU* 2.7 42.3 + - + +
276K ALA* 4.0 10.3 - - + +
279K GLU* 3.6 31.7 + - - -
452K ILE 3.1 8.5 + - - +
453K TYR* 2.9 13.3 + - + +
455K THR* 1.3 79.0 - - - +
457K ASN* 1.3 65.2 + - - +
459K TYR* 2.8 9.8 + - - +
460K SER* 2.8 29.5 + - - +
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Residues in contact with ASN 457 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LYS* 5.4 0.6 - - - +
401K VAL* 3.5 17.2 - - + +
453K TYR* 3.1 60.5 + - - +
454K GLU* 3.4 15.0 + - - +
456K LYS* 1.3 82.2 - - - +
458K GLY* 1.3 53.9 + - - +
460K SER* 2.8 10.7 + - - +
461K ALA* 2.7 37.9 + - - +
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Residues in contact with GLY 458 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339K LEU* 4.8 3.8 - - - +
367K ILE* 4.7 7.6 - - - -
396K LEU* 3.4 31.9 - - - +
401K VAL* 3.8 4.4 - - - +
454K GLU 2.8 14.1 + - - -
455K THR 2.9 5.1 + - - -
457K ASN* 1.3 78.4 - - - +
459K TYR* 1.3 65.7 + - - +
461K ALA 3.5 12.1 + - - -
462K PHE* 3.8 5.4 + - - +
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Residues in contact with TYR 459 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K LEU* 4.1 17.8 - - + +
269K CYS* 3.8 9.6 - - - -
272K THR* 3.2 24.2 - - - -
273K SER* 3.3 38.4 - - - -
276K ALA* 3.7 11.4 - - + -
339K LEU* 4.0 23.3 - - + -
341K SER* 2.7 33.5 + - - -
367K ILE* 3.8 18.8 - - + -
433K CYS* 4.3 6.1 - - + -
434K GLY 4.1 2.3 + - - -
455K THR* 2.9 24.5 + - + +
456K LYS* 2.8 7.8 + - - +
458K GLY* 1.3 75.2 - - - +
460K SER* 1.3 56.0 + - - +
462K PHE* 2.7 39.2 + - - +
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Residues in contact with SER 460 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276K ALA* 3.8 21.2 - - - +
279K GLU* 5.6 6.3 - - - -
280K MET* 5.6 5.2 - - - -
456K LYS* 2.8 14.5 + - - +
457K ASN* 2.8 34.3 + - - -
459K TYR* 1.3 73.1 - - - +
461K ALA* 1.3 51.0 + - - +
462K PHE 2.7 10.9 + - - -
463K LEU* 3.0 31.1 + - - +
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Residues in contact with ALA 461 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395K ILE* 2.9 29.4 - - + +
396K LEU* 4.4 11.4 - - + +
399K GLU* 3.6 36.5 - - + +
401K VAL* 4.7 2.5 - - + -
457K ASN 2.7 23.7 + - - +
458K GLY 3.7 7.4 - - - +
459K TYR 3.1 0.6 + - - -
460K SER* 1.3 70.3 + - - +
462K PHE* 1.3 57.1 + - - +
463K LEU* 3.5 9.2 - - - -
464K ASN 4.0 1.9 - - - +
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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