Contacts of the helix formed by residues 72 - 90 (chain f) 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 f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69f ASP 5.5 2.7 - - - -
70f ILE 3.6 5.4 + - - -
71f ASN* 1.3 74.4 - - - +
73f SER* 1.3 62.0 + - - +
74f GLN* 3.3 7.2 - - - -
75f VAL* 3.8 14.2 - - - +
76f LEU* 2.8 31.7 + - - +
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Residues in contact with SER 73 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72f THR* 1.3 74.0 - - - +
74f GLN* 1.3 58.1 + - - +
76f LEU* 3.9 3.4 - - - +
77f LYS* 2.9 31.9 + - - +
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Residues in contact with GLN 74 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72f THR* 3.3 3.8 - - - -
73f SER* 1.3 76.4 - - - +
75f VAL* 1.3 61.0 + - - +
77f LYS* 3.8 4.8 - - - +
78f LEU* 2.9 33.1 + - - +
157f TYR 5.9 1.1 - - - -
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Residues in contact with VAL 75 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70f ILE 4.1 20.2 - - - +
71f ASN* 5.3 0.2 - - - -
72f THR* 3.4 16.4 + - - +
73f SER 3.4 0.4 - - - -
74f GLN* 1.3 79.2 - - - +
76f LEU* 1.3 57.2 + - - +
78f LEU* 3.9 3.7 - - - +
79f LEU* 2.9 30.1 + - - +
154f ILE* 5.5 8.3 - - + +
157f TYR* 5.0 17.3 - - + +
158f LEU* 6.2 0.7 - - - +
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Residues in contact with LEU 76 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71f ASN* 5.9 3.4 - - + -
72f THR 2.8 19.2 + - - +
73f SER* 4.2 2.9 - - - +
75f VAL* 1.3 74.3 - - - +
77f LYS* 1.3 61.7 + - - +
79f LEU* 3.7 5.8 - - - +
80f HIS* 2.9 29.8 + - - +
135f VAL 4.9 13.1 - - - +
136f ARG* 5.8 5.8 - - + -
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Residues in contact with LYS 77 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73f SER 2.9 20.9 + - - +
74f GLN* 3.8 5.8 - - - +
76f LEU* 1.3 77.2 - - - +
78f LEU* 1.3 58.1 + - - +
80f HIS* 3.2 7.3 + - - +
81f THR* 2.9 27.6 + - - -
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Residues in contact with LEU 78 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74f GLN 2.9 17.6 + - - +
75f VAL 4.2 2.5 - - - +
77f LYS* 1.3 76.8 - - - +
79f LEU* 1.3 57.8 + - - +
81f THR* 3.4 9.1 + - - -
82f ASP* 2.9 27.2 + - - +
157f TYR* 4.6 23.3 - - + +
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Residues in contact with LEU 79 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75f VAL 2.9 21.2 + - - +
76f LEU* 3.7 7.6 - - - +
78f LEU* 1.3 74.8 - - - +
80f HIS* 1.3 58.4 + - - +
82f ASP* 3.1 7.2 + - - +
83f ILE* 2.9 28.5 + - - +
157f TYR* 5.7 2.6 - - + +
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Residues in contact with HIS 80 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76f LEU 2.9 18.2 + - - +
77f LYS* 3.2 6.9 + - - +
79f LEU* 1.3 75.5 - - - +
81f THR* 1.3 57.4 + - - +
83f ILE* 3.3 7.2 + - - +
84f VAL* 2.9 28.6 + - - +
127f LEU* 5.7 9.7 - - + +
130f ILE* 4.8 19.7 - - + +
131f LYS* 5.9 1.3 - - - +
135f VAL* 6.4 3.4 - - + -
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Residues in contact with THR 81 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77f LYS 2.9 13.8 + - - -
78f LEU* 3.6 12.1 - - - -
79f LEU 3.2 0.2 - - - -
80f HIS* 1.3 77.7 - - - +
82f ASP* 1.3 56.4 + - - +
84f VAL* 3.3 7.6 + - - +
85f SER* 2.9 27.7 + - - -
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Residues in contact with ASP 82 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78f LEU 2.9 14.7 + - - +
79f LEU* 3.1 11.6 + - - +
81f THR* 1.3 77.2 - - - +
83f ILE* 1.3 57.2 + - - +
85f SER* 3.2 8.4 + - - -
86f GLN* 2.9 26.9 + - - +
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Residues in contact with ILE 83 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79f LEU 2.9 15.8 + - - +
80f HIS* 3.7 8.1 - - - +
82f ASP* 1.3 76.5 - - - +
84f VAL* 1.3 56.9 + - - +
86f GLN* 3.2 8.4 + - - +
87f LEU* 2.9 28.9 + - - +
130f ILE* 5.9 5.6 - - + -
111g GLU* 5.7 6.7 - - + +
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Residues in contact with VAL 84 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80f HIS 2.9 18.0 + - - +
81f THR* 3.6 8.5 - - - +
82f ASP 3.3 0.2 - - - -
83f ILE* 1.3 76.0 - - - +
85f SER* 1.3 57.7 + - - +
87f LEU* 3.5 6.9 + - - +
88f ASN* 2.9 28.6 + - - +
126f LEU* 5.4 13.5 - - + -
127f LEU* 5.5 11.9 - - + +
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Residues in contact with SER 85 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81f THR 2.9 13.6 + - - -
82f ASP* 3.5 11.0 - - - -
84f VAL* 1.3 74.6 - - - +
86f GLN* 1.3 58.9 + - - +
88f ASN* 3.1 7.5 + - - +
89f ASP* 2.9 29.3 + - - +
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Residues in contact with GLN 86 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82f ASP 2.9 13.3 + - - +
83f ILE* 3.2 11.9 + - - +
85f SER* 1.3 77.6 - - - +
87f LEU* 1.3 61.2 + - - +
89f ASP* 3.4 18.1 + - - +
90f LYS* 4.0 7.3 + - - +
111g GLU* 5.7 9.4 - - + +
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Residues in contact with LEU 87 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83f ILE 2.9 16.2 + - - +
84f VAL* 3.8 7.2 - - - +
86f GLN* 1.3 76.8 - - - +
88f ASN* 1.3 60.2 + - - +
89f ASP 3.6 0.2 + - - -
90f LYS* 3.3 20.7 + - - +
93f VAL* 5.0 6.2 - - + +
94f ARG* 3.8 14.6 + - + +
126f LEU* 6.2 4.0 - - + -
111g GLU* 5.7 8.4 - - + +
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Residues in contact with ASN 88 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84f VAL 2.9 17.8 + - - +
85f SER* 3.1 8.5 + - - +
87f LEU* 1.3 74.6 - - - +
89f ASP* 1.3 63.2 + - - +
90f LYS 3.2 5.9 + - - +
91f PRO* 4.7 1.9 - - - +
94f ARG* 5.0 5.4 - - - -
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Residues in contact with ASP 89 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85f SER 2.9 14.4 + - - +
86f GLN* 3.7 10.5 - - - +
87f LEU 3.3 1.0 - - - -
88f ASN* 1.3 77.1 - - - +
90f LYS* 1.3 57.9 + - + +
91f PRO 3.9 2.3 - - - -
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Residues in contact with LYS 90 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86f GLN 4.0 5.5 + - - +
87f LEU* 3.3 18.5 + - - +
88f ASN 3.2 2.7 - - - +
89f ASP* 1.3 78.4 - - + +
91f PRO* 1.3 64.5 - - - +
92f GLU* 3.4 1.3 - - + +
93f VAL* 4.3 19.3 - - + +
94f ARG* 3.3 11.1 + - - +
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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