Contacts of the helix formed by residues 73 - 85 (chain S) in PDB entry 5GJQ
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 GLU 73 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S THR 3.5 0.8 + - - -
72S LEU* 1.3 74.7 - - + +
74S ASP* 1.3 66.1 + - - +
75S ILE 3.1 0.7 - - - -
76S LYS* 3.0 28.4 + - + +
77S GLU* 3.2 6.4 + - - +
205S LEU* 6.0 2.2 - - - -
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Residues in contact with ASP 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S ASP* 3.4 28.3 - - + +
70S VAL* 4.9 4.7 - - + +
71S THR 3.4 20.2 + - - +
72S LEU 2.8 0.8 + - - -
73S GLU* 1.3 75.6 - - - +
75S ILE* 1.3 51.2 + - - +
77S GLU* 3.0 11.1 + - - +
78S HIS* 2.4 37.2 + - - +
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Residues in contact with ILE 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S ASP 3.9 5.9 + - - +
72S LEU 2.9 14.6 + - - +
74S ASP* 1.3 75.3 - - - +
76S LYS* 1.3 52.8 + - - +
78S HIS* 3.0 11.4 + - - +
79S VAL* 2.6 37.7 + - - +
202S ALA* 5.7 7.0 - - + +
205S LEU* 4.8 13.2 - - + -
206S VAL* 6.3 3.4 - - + +
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Residues in contact with LYS 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72S LEU 4.3 0.2 + - - -
73S GLU* 3.0 21.0 + - + +
75S ILE* 1.3 80.5 - - - +
77S GLU* 1.3 62.6 + - - +
79S VAL* 3.0 15.1 + - - +
80S LYS* 3.1 11.0 + - - +
205S LEU* 4.7 15.4 - - + +
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Residues in contact with GLU 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S ASP* 6.1 0.2 - - + -
73S GLU 3.2 5.0 + - - +
74S ASP* 3.0 12.0 + - - +
76S LYS* 1.3 76.6 - - - +
78S HIS* 1.3 64.8 + - - +
80S LYS* 3.0 25.2 + - - +
81S GLN* 3.8 5.0 + - - +
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Residues in contact with HIS 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65S ARG* 4.3 14.8 - - + +
68S ASP* 3.1 34.9 - - + +
74S ASP 2.4 23.2 + - - +
75S ILE* 3.1 17.5 - - - +
77S GLU* 1.3 68.6 - - - +
79S VAL* 1.3 58.8 + - - +
81S GLN* 4.1 1.7 + - - +
82S LEU* 3.0 22.3 + - - +
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Residues in contact with VAL 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S ILE 2.6 15.2 + - - +
76S LYS* 3.0 12.3 + - - +
78S HIS* 1.3 73.7 - - - +
80S LYS* 1.3 52.6 + - - +
82S LEU* 2.9 8.9 + - - +
83S GLU* 2.6 35.8 + - - +
209S LYS* 4.4 27.7 - - + -
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Residues in contact with LYS 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S LYS 3.1 9.7 + - - +
77S GLU* 3.0 17.1 + - - +
79S VAL* 1.3 73.3 - - - +
81S GLN* 1.3 59.1 + - - +
83S GLU* 2.9 29.0 + - - +
3Y GLU 4.7 16.6 - - - +
5Y LYS* 3.6 14.4 - - + +
6Y GLN* 5.2 11.7 - - + +
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Residues in contact with GLN 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77S GLU 3.8 4.6 + - - +
78S HIS 4.9 2.0 - - - +
79S VAL 3.5 0.2 - - - -
80S LYS* 1.3 78.8 - - - +
82S LEU* 1.3 50.4 + - - +
83S GLU 2.9 0.2 - - - -
84S LYS* 2.7 12.1 + - - +
85S ALA* 2.6 33.4 + - + +
5Y LYS* 5.0 4.3 - - - -
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Residues in contact with LEU 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65S ARG* 5.4 8.3 - - + -
78S HIS 3.0 21.4 + - - +
79S VAL* 2.9 11.2 + - - +
81S GLN* 1.3 76.4 - - - +
83S GLU* 1.3 62.5 + - - +
85S ALA* 3.3 25.6 + - + +
86S VAL* 4.1 5.2 + - - +
166S TYR* 6.1 5.2 - - + -
169S LEU* 6.6 0.4 - - + -
170S LEU* 5.4 11.5 - - + +
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Residues in contact with GLU 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S VAL 2.6 13.2 + - - +
80S LYS* 2.9 17.5 + - - +
82S LEU* 1.3 76.6 - - - +
84S LYS* 1.3 56.0 + - - +
86S VAL* 4.4 9.5 + - - +
209S LYS* 5.7 5.6 - - - +
213S TYR* 5.3 4.4 + - - -
5Y LYS* 4.0 13.5 - - + +
6Y GLN* 4.6 2.5 - - - +
9Y ASP* 3.9 29.0 - - + +
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Residues in contact with LYS 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81S GLN* 2.7 11.2 + - - +
83S GLU* 1.3 74.0 - - - +
85S ALA* 1.3 59.5 + - - +
86S VAL 3.1 6.9 + - - -
87S SER* 3.4 19.4 + - - +
5Y LYS* 4.7 15.5 - - + -
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Residues in contact with ALA 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61S GLU* 5.4 13.2 - - + -
62S HIS* 6.1 2.2 - - - +
81S GLN* 2.6 10.9 + - + +
82S LEU* 3.3 30.6 + - + +
84S LYS* 1.3 73.4 - - - +
86S VAL* 1.3 56.9 + - - +
87S SER* 3.3 2.8 + - - -
88S GLY 4.1 12.5 + - - +
170S LEU* 5.2 11.6 - - + +
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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