Contacts of the helix formed by residues 449 - 461 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13M TRP* 4.5 2.7 - - + -
25M PHE* 4.0 18.4 - - + +
26M ALA* 3.5 19.3 + - - +
29M ASP* 5.7 1.1 - - + +
30M ARG* 3.0 39.2 - - + +
251M ASP* 2.6 28.3 + - - -
256M ARG* 2.8 30.0 + - - +
257M SER* 3.0 15.3 + - - +
258M MET 3.6 9.6 - - - -
259M VAL* 3.7 14.8 - - + -
447M SER 3.7 1.2 + - - -
448M SER* 1.3 71.1 - - - +
450M ALA* 1.3 64.6 + - - +
452M ILE* 3.1 14.0 + - + +
453M TYR* 2.9 24.6 + - - +
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Residues in contact with ALA 450 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M ALA* 3.6 11.9 - - + -
13M TRP* 3.4 38.4 - - + +
16M TYR* 2.9 32.2 + - + -
25M PHE* 3.9 5.4 - - - -
364M GLY* 4.9 1.6 - - - -
448M SER* 3.1 5.0 + - - +
449M LYS* 1.3 79.7 - - - +
451M ASP* 1.3 57.0 + - - +
453M TYR 3.3 0.2 + - - -
454M GLU* 2.8 27.5 + - - +
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Residues in contact with ASP 451 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362M TYR 4.2 1.6 - - - +
363M LEU* 3.6 4.5 - - - +
364M GLY* 2.6 35.2 + - - -
365M LYS 3.2 0.4 + - - -
366M GLY 2.8 42.1 + - - +
404M GLN* 5.0 0.2 - - - -
435M VAL* 3.5 21.6 - - + +
436M ALA* 4.7 6.6 - - - +
448M SER* 2.8 24.2 + - - +
450M ALA* 1.3 70.7 - - - +
452M ILE* 1.3 67.1 + - - +
454M GLU* 3.7 5.5 - - - +
455M THR* 2.7 29.9 + - - +
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Residues in contact with ILE 452 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M ASP* 4.1 22.7 - - + -
30M ARG* 5.8 3.4 - - - +
33M ASN* 3.9 23.8 - - + +
259M VAL* 4.2 12.3 - - + -
268M ILE* 3.7 22.2 - - + -
272M THR* 3.7 25.7 - - + +
435M VAL* 4.3 6.0 - - + +
447M SER* 3.9 16.4 - - - +
448M SER 2.8 16.7 + - - +
449M LYS* 3.3 22.9 - - + +
451M ASP* 1.3 77.8 - - - +
453M TYR* 1.3 65.7 + - - +
455M THR* 3.4 6.3 - - - -
456M LYS* 3.1 14.7 + - - +
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Residues in contact with TYR 453 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M LYS* 5.3 0.4 - - - -
16M TYR* 3.0 43.3 - + - -
21M LEU* 3.1 28.9 - - + +
24M VAL* 4.0 22.3 - - + +
25M PHE* 3.4 44.9 - + + -
29M ASP* 3.6 15.9 + - - +
449M LYS 2.9 12.6 + - - +
450M ALA 3.4 6.5 - - - +
452M ILE* 1.3 74.6 - - - +
454M GLU* 1.3 62.9 + - - +
456M LYS* 2.8 19.1 + - + +
457M ASN* 3.1 44.3 + - - -
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Residues in contact with GLU 454 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M ALA* 3.5 10.9 - - - +
15M LYS* 2.8 20.3 + - - -
16M TYR* 2.5 30.5 + - - -
366M GLY* 3.9 13.0 - - - -
367M ILE* 4.4 1.3 - - - +
401M VAL* 3.5 14.6 - - + +
402M ASN* 3.1 56.9 + - + +
450M ALA 2.8 18.1 + - - +
451M ASP 3.7 2.9 - - - +
453M TYR* 1.3 71.5 - - - +
455M THR* 1.3 56.8 - - - +
457M ASN* 3.1 14.2 + - - +
458M GLY 2.8 24.4 + - - -
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Residues in contact with THR 455 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269M CYS* 5.3 0.2 - - - -
272M THR* 3.7 9.4 - - - +
367M ILE* 3.5 30.9 - - + +
434M GLY 5.1 1.1 - - - -
435M VAL* 3.5 26.2 - - + +
451M ASP 2.7 23.2 + - - -
452M ILE 3.4 4.5 - - - -
454M GLU* 1.3 71.3 - - - +
456M LYS* 1.3 65.0 + - - +
458M GLY* 2.9 3.6 + - - -
459M TYR* 2.9 57.7 + - + +
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Residues in contact with LYS 456 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M ASP* 4.1 19.0 + - - +
32M LYS* 4.8 3.0 - - - +
272M THR* 3.9 31.2 - - + +
275M GLU* 2.7 42.9 + - + +
276M ALA* 4.0 10.1 - - + +
279M GLU* 3.5 30.6 + - - -
452M ILE 3.1 7.6 + - - +
453M TYR* 2.8 14.5 + - + +
455M THR* 1.3 79.5 - - - +
457M ASN* 1.3 63.6 + - - +
459M TYR* 2.8 8.9 + - - +
460M SER* 2.8 30.4 + - - +
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Residues in contact with ASN 457 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M LYS* 5.4 0.6 - - - +
401M VAL* 3.5 17.4 - - + +
453M TYR* 3.1 60.3 + - - +
454M GLU* 3.4 14.8 + - - +
456M LYS* 1.3 83.0 - - - +
458M GLY* 1.3 52.6 + - - +
460M SER* 2.8 11.3 + - - +
461M ALA* 2.7 37.4 + - - +
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Residues in contact with GLY 458 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339M LEU* 4.8 3.9 - - - +
367M ILE* 4.7 8.1 - - - -
396M LEU* 3.4 31.3 - - - +
401M VAL* 3.8 4.4 - - - +
454M GLU 2.8 14.4 + - - -
455M THR 2.9 6.0 + - - -
457M ASN* 1.3 78.3 - - - +
459M TYR* 1.3 65.2 + - - +
461M ALA 3.5 12.8 + - - -
462M PHE* 3.8 5.0 + - - +
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Residues in contact with TYR 459 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M LEU* 4.1 16.9 - - + +
269M CYS* 3.7 9.4 - - - -
272M THR* 3.2 25.4 - - - -
273M SER* 3.3 38.1 - - - -
276M ALA* 3.7 11.7 - - + -
339M LEU* 4.0 24.0 - - + -
341M SER* 2.7 34.7 + - - -
367M ILE* 3.8 19.3 - - + -
433M CYS* 4.3 6.5 - - + -
434M GLY 4.1 1.9 + - - -
455M THR* 2.9 24.5 + - + +
456M LYS* 2.8 7.4 + - - +
458M GLY* 1.3 73.3 - - - +
460M SER* 1.3 57.0 + - - +
462M PHE* 2.7 38.7 + - - +
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Residues in contact with SER 460 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276M ALA* 3.8 23.4 - - - +
279M GLU* 5.6 7.2 - - - -
280M MET* 5.6 4.7 - - - -
456M LYS* 2.8 14.9 + - - +
457M ASN* 2.8 34.0 + - - -
459M TYR* 1.3 72.3 - - - +
461M ALA* 1.3 55.4 + - - +
462M PHE 2.7 6.2 + - - -
463M LEU* 3.1 31.4 + - - +
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Residues in contact with ALA 461 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395M ILE* 2.9 28.6 - - + +
396M LEU* 4.4 11.5 - - + +
399M GLU* 3.6 37.4 - - + +
401M VAL* 4.7 1.8 - - + -
457M ASN 2.7 23.1 + - - +
458M GLY 3.7 7.7 - - - +
459M TYR 3.1 0.8 + - - -
460M SER* 1.3 71.4 + - - +
462M PHE* 1.3 56.9 + - - +
463M LEU* 3.5 9.0 - - - -
464M ASN 4.5 1.7 - - - +
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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