Contacts of the helix formed by residues 449 - 461 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D TRP* 4.5 3.1 - - + -
25D PHE* 3.9 18.3 - - + +
26D ALA* 3.4 19.6 + - - +
29D ASP* 5.7 0.9 - - - +
30D ARG* 3.0 39.6 - - + +
251D ASP* 2.6 28.5 + - - -
256D ARG* 2.8 30.2 + - - +
257D SER* 3.0 15.4 + - - +
258D MET 3.7 9.9 - - - -
259D VAL* 3.7 14.4 - - + -
447D SER 3.8 1.2 + - - -
448D SER* 1.3 70.1 - - - +
450D ALA* 1.3 64.7 + - - +
452D ILE* 3.1 13.8 + - + +
453D TYR* 2.9 24.9 + - - +
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Residues in contact with ALA 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 3.6 12.6 - - + -
13D TRP* 3.4 37.3 - - + +
16D TYR* 2.9 33.8 + - + -
25D PHE* 3.9 5.4 - - - -
364D GLY* 4.9 1.3 - - - -
448D SER* 3.1 5.2 + - - +
449D LYS* 1.3 79.3 - - - +
451D ASP* 1.3 57.1 + - - +
453D TYR* 3.4 0.5 + - - +
454D GLU* 2.8 27.5 + - - +
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Residues in contact with ASP 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D TYR 4.2 1.6 - - - +
363D LEU* 3.6 3.8 - - - +
364D GLY* 2.5 34.1 + - - -
365D LYS 3.2 0.4 + - - -
366D GLY 2.9 41.4 + - - +
404D GLN* 5.0 0.2 - - - -
435D VAL* 3.4 22.1 - - + +
436D ALA* 4.7 6.9 - - - +
448D SER* 2.7 24.7 + - - +
450D ALA* 1.3 69.4 - - - +
452D ILE* 1.3 67.8 + - - +
454D GLU* 3.2 5.4 + - - +
455D THR* 2.7 30.1 + - - +
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Residues in contact with ILE 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASP* 4.1 23.1 - - + -
30D ARG* 5.7 3.8 - - - +
33D ASN* 3.9 23.3 - - + +
259D VAL* 4.2 12.3 - - + -
268D ILE* 3.7 21.1 - - + -
272D THR* 3.7 25.5 - - + +
435D VAL* 4.2 6.5 - - + +
447D SER* 4.0 16.8 - - - +
448D SER 2.8 20.9 + - - +
449D LYS* 3.3 22.7 - - + +
451D ASP* 1.3 73.6 - - - +
453D TYR* 1.3 67.7 + - - +
455D THR* 3.2 6.6 + - - -
456D LYS* 3.1 14.9 + - - +
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Residues in contact with TYR 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LYS* 5.3 0.2 - - - -
16D TYR* 3.1 43.1 - + - +
21D LEU* 3.1 28.6 - - + +
24D VAL* 4.0 22.0 - - + +
25D PHE* 3.4 43.1 - + + -
29D ASP* 3.6 15.9 + - + +
449D LYS 2.9 11.8 + - - +
450D ALA 3.4 6.1 - - - +
452D ILE* 1.3 75.4 - - - +
454D GLU* 1.3 63.4 - - - +
456D LYS* 2.9 17.9 + - + +
457D ASN* 3.1 47.3 + - - -
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Residues in contact with GLU 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 3.5 10.6 - - - +
15D LYS* 2.7 20.6 + - - -
16D TYR* 2.4 30.8 + - - -
366D GLY* 3.9 13.2 - - - -
367D ILE* 4.9 0.9 - - - -
401D VAL* 3.4 14.5 - - + +
402D ASN* 3.0 56.4 + - + +
450D ALA 2.8 17.9 + - - +
451D ASP* 3.6 3.1 - - - +
453D TYR* 1.3 72.0 - - - +
455D THR* 1.3 58.0 + - - +
457D ASN* 3.1 14.2 + - - +
458D GLY 2.8 25.3 + - - -
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Residues in contact with THR 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D CYS* 5.3 0.4 - - - -
272D THR* 3.6 13.7 - - - +
367D ILE* 3.5 31.4 - - + +
434D GLY 5.1 0.9 - - - -
435D VAL* 3.4 27.3 - - + +
451D ASP 2.7 18.4 + - - -
452D ILE 3.3 9.2 - - - -
454D GLU* 1.3 71.7 - - - +
456D LYS* 1.3 65.5 + - - +
458D GLY* 2.9 3.3 + - - -
459D TYR* 2.9 53.7 + - + +
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Residues in contact with LYS 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASP* 4.0 18.8 + - - +
32D LYS* 4.7 3.8 - - - +
272D THR* 3.9 30.5 - - + +
275D GLU* 2.7 41.1 + - + +
276D ALA* 4.0 10.5 - - + +
279D GLU* 3.5 31.4 + - - -
452D ILE 3.1 7.1 + - - +
453D TYR* 2.9 13.9 + - + +
455D THR* 1.3 78.0 - - - +
457D ASN* 1.3 66.8 + - - +
459D TYR* 2.8 8.6 + - - +
460D SER* 2.8 31.1 + - - +
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Residues in contact with ASN 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LYS* 5.4 1.0 - - - +
401D VAL* 3.5 17.7 - - + +
453D TYR* 3.1 60.1 + - - +
454D GLU* 3.5 14.8 + - - +
456D LYS* 1.3 81.8 - - - +
458D GLY* 1.3 53.9 + - - +
460D SER* 2.8 11.1 + - - +
461D ALA* 2.7 37.6 + - - +
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Residues in contact with GLY 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D LEU* 4.9 3.5 - - - +
367D ILE* 4.8 8.1 - - - -
396D LEU* 3.4 31.8 - - - +
401D VAL* 3.8 3.8 - - - +
454D GLU 2.8 15.0 + - - -
455D THR 2.9 5.1 + - - -
457D ASN* 1.3 77.2 - - - +
459D TYR* 1.3 67.4 + - - +
461D ALA 3.5 12.0 + - - -
462D PHE* 3.7 5.4 + - - +
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Residues in contact with TYR 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LEU* 4.1 17.1 - - + +
269D CYS* 3.7 9.8 - - - -
272D THR* 3.1 25.1 - - - -
273D SER* 3.3 37.7 - - - -
276D ALA* 3.7 11.9 - - + -
339D LEU* 4.0 23.6 - - + -
341D SER* 2.7 33.4 + - - -
367D ILE* 3.8 19.5 - - + -
433D CYS* 4.4 5.8 - - + -
434D GLY 4.1 2.1 + - - -
455D THR* 2.9 24.0 + - + +
456D LYS 2.8 6.9 + - - +
458D GLY* 1.3 73.5 - - - +
460D SER* 1.3 56.4 + - - +
462D PHE* 2.7 40.1 + - - +
463D LEU 4.1 0.2 + - - -
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Residues in contact with SER 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D ALA* 3.8 22.3 - - - +
279D GLU* 5.6 6.5 - - - -
280D MET* 5.5 5.6 - - - -
456D LYS* 2.8 14.0 + - - +
457D ASN* 2.8 31.4 + - - -
459D TYR* 1.3 72.5 - - - +
461D ALA* 1.3 50.6 + - - +
462D PHE 2.7 11.1 + - - -
463D LEU* 3.0 31.6 + - - +
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Residues in contact with ALA 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D ILE* 2.8 28.8 - - + +
396D LEU* 4.4 11.1 - - + +
399D GLU* 3.6 36.5 - - + +
401D VAL* 4.7 2.0 - - + -
457D ASN 2.7 22.9 + - - +
458D GLY 3.7 7.7 - - - +
459D TYR 3.0 0.4 + - - -
460D SER* 1.3 70.1 + - - +
462D PHE* 1.3 56.7 - - - +
463D LEU* 3.5 11.0 - - - -
464D ASN 4.8 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