Contacts of the helix formed by residues 72 - 90 (chain b) in PDB entry 6QY3
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 THR 72 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122 A 6.0 1.3 - - - -
69b ASP 5.5 2.7 - - - -
70b ILE 3.6 5.1 + - - -
71b ASN* 1.3 74.8 - - - +
73b SER* 1.3 61.7 + - - +
74b GLN* 3.3 7.0 - - - -
75b VAL* 3.8 14.0 - - - +
76b LEU* 2.8 31.7 + - - +
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Residues in contact with SER 73 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122 A 4.0 26.8 - - - -
132 A 3.3 18.8 - - - -
72b THR* 1.3 73.5 - - - +
74b GLN* 1.3 58.2 + - - +
76b LEU* 4.1 3.3 - - - +
77b LYS* 2.9 31.0 + - - +
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Residues in contact with GLN 74 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132 A 3.4 17.5 + - - +
72b THR* 3.3 3.9 - - - -
73b SER* 1.3 75.8 - - - +
75b VAL* 1.3 60.5 + - - +
77b LYS* 3.8 4.2 - - - +
78b LEU* 2.9 33.3 + - - +
157b TYR 5.5 1.4 - - - +
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Residues in contact with VAL 75 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70b ILE 4.1 20.4 - - - +
71b ASN* 5.3 0.2 - - - -
72b THR* 3.4 15.6 + - - +
73b SER 3.4 0.2 - - - -
74b GLN* 1.3 79.4 - - - +
76b LEU* 1.3 57.0 + - - +
78b LEU* 3.9 3.7 - - - +
79b LEU* 2.9 30.7 + - - +
154b ILE* 5.5 8.1 - - + +
157b TYR* 5.0 18.0 - - + +
158b LEU 6.2 0.2 - - - +
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Residues in contact with LEU 76 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71b ASN* 6.0 3.1 - - + +
72b THR 2.8 19.9 + - - +
73b SER* 4.2 3.6 - - - +
75b VAL* 1.3 73.4 - - - +
77b LYS* 1.3 60.6 + - - +
79b LEU* 3.7 5.6 - - - +
80b HIS* 2.9 28.9 + - - +
135b VAL 4.9 13.2 - - - +
136b ARG* 5.8 5.6 - - + -
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Residues in contact with LYS 77 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132 A 5.7 0.7 - - - +
73b SER 2.9 20.6 + - - +
74b GLN* 3.8 4.9 - - - +
76b LEU* 1.3 77.2 - - - +
78b LEU* 1.3 57.5 + - - +
80b HIS* 3.2 7.9 + - - +
81b THR* 2.9 27.3 + - - -
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Residues in contact with LEU 78 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74b GLN 2.9 18.3 + - - +
75b VAL 4.2 2.5 - - - +
77b LYS* 1.3 76.7 - - - +
79b LEU* 1.3 58.3 + - - +
81b THR* 3.4 8.9 + - - -
82b ASP* 2.9 27.5 + - - +
157b TYR* 4.6 22.9 - - + +
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Residues in contact with LEU 79 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75b VAL 2.9 21.0 + - - +
76b LEU* 3.7 7.4 - - - +
77b LYS 3.2 0.2 - - - -
78b LEU* 1.3 74.8 - - - +
80b HIS* 1.3 60.6 + - - +
82b ASP* 3.1 8.5 + - - +
83b ILE* 2.9 27.5 + - - +
157b TYR* 5.7 2.6 - - + +
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Residues in contact with HIS 80 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76b LEU 2.9 18.0 + - - +
77b LYS* 3.2 6.7 + - - +
79b LEU* 1.3 75.9 - - - +
81b THR* 1.3 56.6 + - - +
83b ILE* 3.3 7.4 + - - +
84b VAL* 2.9 28.4 + - - +
127b LEU* 5.7 9.2 - - + +
130b ILE* 4.8 20.1 - - + +
131b LYS* 5.9 2.0 - - + +
135b VAL* 6.4 3.1 - - + -
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Residues in contact with THR 81 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77b LYS 2.9 13.9 + - - -
78b LEU* 3.6 12.6 - - - -
80b HIS* 1.3 77.6 - - - +
82b ASP* 1.3 56.6 + - - +
84b VAL* 3.3 8.8 + - - +
85b SER* 2.9 27.9 + - - -
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Residues in contact with ASP 82 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78b LEU 2.9 15.1 + - - +
79b LEU* 3.5 11.2 - - - +
81b THR* 1.3 77.1 - - - +
83b ILE* 1.3 57.1 + - - +
85b SER* 3.2 7.8 + - - -
86b GLN* 2.9 27.9 + - - +
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Residues in contact with ILE 83 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79b LEU 2.9 15.3 + - - +
80b HIS* 3.7 8.7 - - - +
81b THR 3.3 0.2 - - - -
82b ASP* 1.3 75.9 - - - +
84b VAL* 1.3 57.4 + - - +
86b GLN* 3.2 8.4 + - - +
87b LEU* 2.9 29.7 + - - +
130b ILE* 5.9 5.2 - - + -
111c GLU* 6.2 3.8 - - + -
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Residues in contact with VAL 84 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80b HIS 2.9 17.6 + - - +
81b THR* 3.6 9.2 - - - +
82b ASP 3.3 0.2 - - - -
83b ILE* 1.3 76.5 - - - +
85b SER* 1.3 56.5 + - - +
87b LEU* 3.5 6.6 + - - +
88b ASN* 2.9 28.4 + - - +
126b LEU* 5.4 14.4 - - + -
127b LEU* 5.5 11.9 - - + +
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Residues in contact with SER 85 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81b THR 2.9 14.0 + - - -
82b ASP* 3.5 11.2 - - - -
83b ILE 3.2 0.2 - - - -
84b VAL* 1.3 75.4 - - - +
86b GLN* 1.3 59.6 + - - +
88b ASN* 3.1 7.9 + - - +
89b ASP* 2.9 29.5 + - - +
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Residues in contact with GLN 86 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82b ASP 2.9 13.8 + - - +
83b ILE* 3.2 12.1 + - - +
85b SER* 1.3 76.6 - - - +
87b LEU* 1.3 60.7 + - - +
89b ASP* 3.4 17.1 + - - +
90b LYS* 4.0 6.8 + - - +
111c GLU* 5.7 9.2 - - + +
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Residues in contact with LEU 87 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83b ILE 2.9 16.5 + - - +
84b VAL* 3.8 7.0 - - - +
86b GLN* 1.3 76.8 - - - +
88b ASN* 1.3 60.6 + - - +
89b ASP 3.6 0.2 + - - -
90b LYS* 3.3 21.0 + - - +
93b VAL* 5.0 4.9 - - + +
94b ARG* 3.8 14.3 + - + +
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Residues in contact with ASN 88 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84b VAL 2.9 18.9 + - - +
85b SER* 3.1 9.3 + - - +
87b LEU* 1.3 74.3 - - - +
89b ASP* 1.3 64.2 + - - +
90b LYS 3.2 6.2 + - - +
91b PRO* 4.7 1.6 - - - +
94b ARG* 5.0 6.5 - - - +
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Residues in contact with ASP 89 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85b SER 2.9 15.2 + - - +
86b GLN* 3.7 10.3 - - - +
87b LEU 3.3 0.4 - - - -
88b ASN* 1.3 77.1 - - - +
90b LYS* 1.3 58.8 + - - +
91b PRO 3.9 1.9 - - - -
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Residues in contact with LYS 90 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86b GLN 4.0 6.0 + - - +
87b LEU* 3.3 16.6 + - - +
88b ASN 3.2 2.8 - - - +
89b ASP* 1.3 78.7 - - - +
91b PRO* 1.3 64.4 - - - +
92b GLU* 3.4 1.8 - - + +
93b VAL* 4.3 19.3 - - + +
94b ARG* 3.3 12.1 + - - +
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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