Contacts of the helix formed by residues 70 - 79 (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 GLY 70 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676 CYS* 2.7 33.2 + - - -
686 GLY 3.0 3.1 - - - -
696 THR* 1.3 71.5 - - - +
716 ILE* 1.3 62.8 + - - +
726 LEU 3.3 2.9 - - - -
736 SER* 3.1 11.7 + - - -
746 MET* 2.9 29.8 + - - +
966 ALA* 4.5 6.1 - - - -
1006 VAL* 5.7 2.9 - - - -
1116 LEU* 5.1 4.0 - - - -
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Residues in contact with ILE 71 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1895 VAL* 4.7 2.2 - - + -
1905 TYR* 4.2 15.5 - - + -
1925 PHE* 3.6 33.9 - - + -
1945 TYR* 3.3 19.6 + - - +
376 LEU* 4.0 13.7 - - + -
426 ARG* 4.2 19.7 - - - +
436 THR* 3.9 10.8 - - + -
676 CYS 4.6 5.2 - - - +
696 THR* 3.3 15.7 + - - +
706 GLY* 1.3 75.4 - - - +
726 LEU* 1.3 69.6 + - + +
746 MET* 3.2 9.8 + - - +
756 PHE* 2.9 49.2 + - + -
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Residues in contact with LEU 72 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426 ARG* 4.7 12.1 - - - +
436 THR* 5.1 0.4 - - + -
466 TYR* 3.8 52.7 - - + -
506 ILE* 4.6 1.5 - - + +
646 ASP* 3.4 21.7 + - - +
676 CYS* 5.2 2.4 + - - +
706 GLY 3.3 0.8 - - - -
716 ILE* 1.3 85.8 - - + +
736 SER* 1.3 67.8 + - - +
756 PHE* 3.0 21.0 + - + +
766 ALA* 2.9 23.2 + - - +
1306 ILE* 3.8 19.8 - - + +
1316 SER 4.5 0.9 - - - -
1326 GLU* 4.5 20.0 - - + +
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Residues in contact with SER 73 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646 ASP* 2.6 33.7 + - - +
676 CYS* 4.0 7.8 - - - +
706 GLY* 3.1 11.2 + - - -
726 LEU* 1.3 74.3 - - - +
746 MET* 1.3 58.9 + - - +
766 ALA* 3.1 4.9 + - - +
776 ALA* 2.8 31.2 + - - +
846 VAL* 3.6 24.1 - - - +
866 GLY* 4.4 4.9 - - - -
1006 VAL* 5.9 0.4 - - - -
1096 ILE* 3.5 20.7 - - - +
1116 LEU* 4.8 1.9 - - - +
1306 ILE* 4.7 0.7 - - - -
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Residues in contact with MET 74 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1925 PHE* 3.7 27.5 - - + -
1945 TYR* 3.9 23.3 - - + +
696 THR 3.9 15.9 - - - +
706 GLY 2.9 13.6 + - - +
716 ILE* 3.4 9.6 - - - +
736 SER* 1.3 78.1 - - - +
756 PHE* 1.3 55.6 + - - +
776 ALA* 3.8 0.5 - - - +
786 LYS* 2.8 31.5 + - - +
996 LEU* 3.8 31.6 - - + +
1006 VAL* 4.1 10.1 - - + -
1036 ASN* 3.9 29.2 - - - +
1056 PHE* 4.1 13.5 - - + -
1096 ILE* 3.7 13.5 - - + -
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Residues in contact with PHE 75 (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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1882 ASP* 5.7 0.2 - - - -
1905 TYR* 4.1 17.0 - + + -
1925 PHE* 3.7 22.2 - + - -
436 THR* 3.7 37.2 - - + -
476 ARG* 3.8 43.5 - - + -
506 ILE* 3.8 17.2 - - + +
716 ILE* 2.9 39.4 + - + -
726 LEU* 3.0 21.3 + - + +
746 MET* 1.3 72.1 - - - +
766 ALA* 1.3 63.3 + - - +
786 LYS* 4.4 6.1 - - + -
796 HIS* 2.8 42.3 + + - +
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Residues in contact with ALA 76 (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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506 ILE* 4.3 11.2 - - - +
576 PHE* 3.9 22.5 - - + -
626 VAL* 4.0 21.8 - - + -
726 LEU 2.9 15.2 + - - +
736 SER* 3.5 7.6 - - - +
756 PHE* 1.3 71.9 - - - +
776 ALA* 1.3 60.7 + - - +
796 HIS* 2.8 19.8 + - - +
806 GLY 3.1 15.2 + - - +
816 ALA* 4.3 3.8 - - - -
846 VAL* 4.1 2.5 - - + -
1306 ILE* 4.4 8.5 - - + -
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Residues in contact with ALA 77 (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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736 SER 2.8 19.2 + - - +
746 MET 3.9 2.0 - - - +
766 ALA* 1.3 73.4 - - - +
786 LYS* 1.3 63.0 + - - +
796 HIS 3.3 0.5 + - - -
806 GLY* 3.4 8.3 + - - -
816 ALA* 4.6 7.2 - - - +
846 VAL* 3.8 8.2 - - + +
1056 PHE* 4.0 15.6 - - + -
1086 LYS* 3.9 30.2 + - + +
1096 ILE* 3.6 27.6 - - + -
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Residues in contact with LYS 78 (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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781 LYS* 4.6 22.6 - - - +
1912 GLY* 4.0 22.6 + - - -
1905 TYR 4.5 13.3 + - - -
1915 GLY* 5.3 0.8 - - - -
1925 PHE* 4.1 21.9 - - + -
476 ARG* 6.3 0.4 - - - +
746 MET 2.8 18.3 + - - +
756 PHE* 3.6 7.9 - - + +
776 ALA* 1.3 78.6 - - - +
796 HIS* 1.3 85.0 + - + +
806 GLY 3.4 0.7 + - - -
1056 PHE* 3.8 21.2 - - + -
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Residues in contact with HIS 79 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476 ARG* 5.1 2.0 - - + -
506 ILE* 4.1 20.0 - - + +
516 ILE* 3.6 34.2 - - + +
546 LYS* 4.0 46.4 - - + +
576 PHE* 4.6 1.7 - - + +
586 LYS* 4.5 0.7 + - - -
756 PHE* 2.8 36.7 + + + +
766 ALA 2.8 6.5 + - - +
786 LYS* 1.3 112.5 - - + +
806 GLY* 1.3 59.0 + - - +
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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