Contacts of the helix formed by residues 39 - 54 (chain 6) in PDB entry 1G6Q
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 ASP 39 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1905 TYR* 3.6 1.8 - - - -
356 GLU 3.4 14.3 + - - +
366 MET 3.5 11.9 - - - +
376 LEU 3.2 1.8 - - - -
386 GLN* 1.3 75.3 - - - +
406 THR* 1.3 61.2 + - - +
416 VAL* 3.3 13.2 + - - +
426 ARG* 3.0 27.6 + - + +
436 THR* 3.0 24.9 + - - -
2816 TYR* 4.1 9.0 - - + +
2826 THR* 3.1 24.7 + - - -
2836 HIS* 3.1 31.0 + - + +
2846 TRP* 4.1 0.3 - - - -
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Residues in contact with THR 40 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1842 ASN* 3.5 27.0 + - - +
1905 TYR* 3.1 23.6 - - + +
386 GLN* 3.0 12.6 + - - +
396 ASP* 1.3 69.8 + - - +
416 VAL* 1.3 71.6 + - - +
446 LEU* 3.0 45.8 + - + +
2816 TYR 5.7 0.5 + - - -
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Residues in contact with VAL 41 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396 ASP* 3.3 7.9 + - - +
406 THR* 1.3 79.2 + - - +
426 ARG* 1.3 67.0 + - - +
446 LEU* 4.4 1.1 - - - +
456 SER* 3.0 26.2 + - - +
2736 PHE* 3.4 39.5 - - + -
2746 SER 4.5 7.0 - - - +
2806 PRO* 4.4 24.5 - - + +
2816 TYR 3.6 21.5 + - - +
2826 THR* 4.8 5.6 - - - -
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Residues in contact with ARG 42 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366 MET* 3.4 40.5 + - - +
376 LEU* 4.7 2.8 - - - +
396 ASP* 3.0 22.3 + - - +
416 VAL* 1.3 83.1 - - - +
436 THR* 1.3 99.8 + - - +
456 SER* 3.0 10.2 + - - -
466 TYR* 3.3 20.2 + - + -
716 ILE* 4.2 21.4 - - - +
726 LEU* 4.7 9.7 - - - +
1326 GLU* 3.1 44.6 + - + +
2736 PHE* 4.7 10.7 - - + -
2836 HIS* 4.1 13.0 - - - -
2846 TRP* 4.0 17.9 - - + -
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Residues in contact with THR 43 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1905 TYR* 3.1 41.2 + - + -
366 MET 3.5 4.2 + - - -
376 LEU* 4.2 1.1 - - + -
396 ASP 3.0 14.9 + - - -
426 ARG* 1.3 101.9 + - - +
446 LEU* 1.3 52.5 + - - +
466 TYR* 3.0 9.8 + - - +
476 ARG* 2.8 31.9 + - - +
716 ILE* 3.9 11.2 - - + -
726 LEU* 5.1 1.6 - - + -
756 PHE* 3.7 23.8 - - + -
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Residues in contact with LEU 44 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1842 ASN* 4.3 8.7 - - - +
1872 GLN* 3.9 25.6 - - + +
1882 ASP* 4.1 10.3 - - + +
1905 TYR* 3.7 29.2 - - + -
406 THR* 3.0 35.1 + - + +
416 VAL* 4.4 1.1 - - - +
436 THR* 1.3 72.0 - - - +
456 SER* 1.3 60.8 + - - +
476 ARG* 3.5 32.7 - - + +
486 ASN* 2.8 42.3 + - - +
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Residues in contact with SER 45 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416 VAL* 3.0 21.3 + - - +
426 ARG 3.0 5.8 + - - -
446 LEU* 1.3 75.1 - - - +
466 TYR* 1.3 63.3 + - - +
486 ASN* 4.6 1.3 - - - +
496 ALA* 2.9 25.8 + - - +
2626 PHE* 3.7 23.1 - - - -
2716 VAL* 3.6 14.0 - - - +
2726 GLU 4.2 4.3 + - - -
2736 PHE* 3.3 28.2 - - - +
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Residues in contact with TYR 46 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426 ARG* 3.6 24.2 - - + -
436 THR* 3.0 8.0 + - - +
456 SER* 1.3 76.8 - - - +
476 ARG* 1.3 63.5 + - - +
496 ALA* 3.6 0.9 - - - +
506 ILE* 3.0 36.3 + - + +
726 LEU* 3.8 40.2 - - + -
756 PHE* 4.8 0.4 - - + -
1306 ILE* 5.1 3.1 - - + -
1316 SER 2.8 30.4 + - - -
1326 GLU* 3.5 24.5 - - + -
1346 MET* 3.7 17.5 - - + +
1626 PHE* 3.4 20.6 - - + -
1636 PRO* 3.3 16.7 - - + +
2626 PHE* 3.8 22.9 - + - -
2736 PHE* 5.2 3.6 - + - -
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Residues in contact with ARG 47 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1872 GLN* 3.1 41.7 + - - +
1882 ASP* 3.3 24.0 + - - -
1912 GLY 4.2 5.8 + - - -
1932 ASP* 4.0 27.2 + - - +
1905 TYR* 5.8 0.2 - - - -
436 THR 2.8 12.6 + - - +
446 LEU* 3.5 22.8 - - - +
456 SER 3.1 0.2 - - - -
466 TYR* 1.3 77.4 - - - +
486 ASN* 1.3 83.6 + - - +
506 ILE* 3.1 4.0 + - - +
516 ILE* 2.9 52.8 + - + +
756 PHE* 3.8 40.5 - - + -
786 LYS* 6.3 0.7 - - - +
796 HIS* 5.1 2.6 - - + -
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Residues in contact with ASN 48 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1872 GLN* 3.2 25.1 - - - +
446 LEU* 2.8 27.4 + - - +
456 SER* 3.8 3.5 - - - +
476 ARG* 1.3 100.3 + - - +
496 ALA* 1.3 67.6 + - - +
516 ILE* 3.3 9.0 + - - +
526 GLN* 2.9 25.1 + - - +
2716 VAL* 3.7 18.8 - - + +
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Residues in contact with ALA 49 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456 SER 2.9 18.6 + - - +
466 TYR 3.6 3.8 - - - +
486 ASN* 1.3 77.3 - - - +
506 ILE* 1.3 62.4 + - - +
526 GLN* 3.4 1.9 + - - +
536 ASN* 3.0 32.4 + - - +
1626 PHE* 4.2 9.6 - - + -
2626 PHE* 3.6 38.8 - - + -
2716 VAL* 3.4 13.1 - - + +
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Residues in contact with ILE 50 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466 TYR* 3.0 31.5 + - + +
476 ARG* 3.5 4.3 - - - +
496 ALA* 1.3 74.2 - - - +
516 ILE* 1.3 58.4 + - - +
536 ASN 3.0 4.5 + - - -
546 LYS* 2.8 28.6 + - - -
576 PHE* 3.9 38.3 - - + -
726 LEU* 4.6 5.8 - - - +
756 PHE* 3.8 40.2 - - + +
766 ALA* 4.3 4.5 - - - +
796 HIS* 4.1 15.7 - - + +
1306 ILE* 4.6 15.9 - - + -
1626 PHE* 4.7 8.5 - - + -
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Residues in contact with ILE 51 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1932 ASP* 5.8 4.9 - - + +
476 ARG* 2.9 50.0 + - + +
486 ASN* 3.3 11.0 + - - +
506 ILE* 1.3 74.2 - - - +
526 GLN* 1.3 62.6 + - - +
546 LYS* 2.9 44.9 + - + +
796 HIS* 3.6 29.8 - - + +
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Residues in contact with GLN 52 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486 ASN 2.9 20.1 + - - +
496 ALA* 3.6 4.0 - - - +
516 ILE* 1.3 72.0 - - - +
536 ASN* 1.3 64.5 + - - +
546 LYS* 3.4 1.2 + - - +
556 ASP* 4.9 4.7 + - - +
2636 PRO 3.9 5.7 - - - +
2646 ALA* 3.4 23.7 - - - +
2656 PRO* 3.8 19.7 - - + +
2686 LYS* 3.7 39.4 + - + +
2696 ARG 2.8 23.4 + - - +
2716 VAL* 3.4 27.1 + - + +
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Residues in contact with ASN 53 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496 ALA* 3.0 28.0 + - - +
506 ILE 3.2 3.4 - - - +
526 GLN* 1.3 84.1 + - - +
546 LYS* 1.3 62.5 + - - -
556 ASP 3.2 2.7 - - - -
566 LEU* 2.8 35.5 + - + +
576 PHE* 3.2 24.3 + - + -
1606 LEU* 4.7 1.0 - - - +
1626 PHE* 3.5 18.4 - - + -
2636 PRO* 2.9 27.3 + - - +
2646 ALA* 3.9 2.6 - - - -
2656 PRO* 3.3 22.9 - - - +
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Residues in contact with LYS 54 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021 LEU 5.5 4.2 + - - -
1031 ASN 6.2 0.4 - - - -
1041 GLY* 5.9 5.9 - - - +
506 ILE 2.8 14.5 + - - +
516 ILE* 2.9 33.6 + - + +
526 GLN 3.3 1.5 - - - +
536 ASN* 1.3 70.2 - - - +
556 ASP* 1.3 69.8 + - - +
576 PHE* 3.0 9.1 + - - +
586 LYS* 2.8 30.7 + - - +
796 HIS* 4.0 33.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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