Contacts of the helix formed by residues 72 - 90 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ASP* 5.2 5.4 - - - -
70A ILE 3.6 4.3 + - - -
71A ASN* 1.3 75.0 - - - +
73A SER* 1.3 61.4 + - - +
74A GLN* 4.3 4.0 - - - -
75A VAL* 3.8 16.3 - - - +
76A LEU* 2.8 31.6 + - - +
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 1.3 74.4 - - - +
74A GLN* 1.3 56.9 + - - +
76A LEU* 3.9 3.8 - - - +
77A LYS* 2.9 29.5 + - - +
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 3.3 4.1 - - - -
73A SER* 1.3 76.4 - - - +
75A VAL* 1.3 61.6 + - - +
77A LYS* 3.6 6.4 - - - +
78A LEU* 2.9 30.3 + - - +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE 4.0 12.8 - - - +
71A ASN* 5.1 0.4 - - - -
72A THR* 3.4 24.3 + - - +
73A SER 3.4 0.4 - - - -
74A GLN* 1.3 79.5 - - - +
76A LEU* 1.3 56.6 + - - +
78A LEU* 3.4 4.8 + - - +
79A LEU* 2.9 30.7 + - - +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASN* 5.9 3.1 - - + +
72A THR 2.8 22.6 + - - +
73A SER* 4.1 4.3 - - - +
75A VAL* 1.3 71.3 - - - +
77A LYS* 1.3 60.4 + - - +
79A LEU* 3.9 5.2 - - - +
80A HIS* 2.9 31.5 + - - +
135A VAL 5.1 10.4 - - - +
136A ARG* 6.0 5.4 - - + +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A SER 2.9 20.1 + - - +
74A GLN* 3.6 7.4 - - - +
75A VAL 3.2 0.4 - - - -
76A LEU* 1.3 77.8 - - - +
78A LEU* 1.3 58.7 + - - +
80A HIS* 3.9 3.5 - - - +
81A THR* 2.9 30.3 + - - -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLN 2.9 16.5 + - - +
75A VAL* 4.0 4.5 - - - +
77A LYS* 1.3 76.7 - - - +
79A LEU* 1.3 58.3 + - - +
81A THR* 3.8 5.5 - - - -
82A ASP* 2.9 29.5 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL 2.9 18.7 + - - +
76A LEU* 3.9 7.0 - - - +
78A LEU* 1.3 74.8 - - - +
80A HIS* 1.3 60.4 + - - +
82A ASP* 3.2 6.6 + - - +
83A ILE* 2.9 29.3 + - - +
135A VAL 5.7 4.7 - - - +
136A ARG* 6.2 3.4 - - - -
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Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU 2.9 20.0 + - - +
77A LYS* 4.0 4.0 - - - +
79A LEU* 1.3 75.9 - - - +
81A THR* 1.3 58.2 + - - +
83A ILE* 3.4 6.4 + - - +
84A VAL* 2.9 28.6 + - - +
127A LEU* 5.9 5.6 - - + +
130A ILE* 5.0 18.5 - - + +
131A LYS* 6.0 1.3 - - + +
135A VAL* 6.4 2.7 - - + -
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS 2.9 19.2 + - - -
78A LEU* 3.9 6.5 - - - -
80A HIS* 1.3 76.1 - - - +
82A ASP* 1.3 58.0 + - - +
84A VAL* 3.4 6.8 + - - +
85A SER* 2.9 27.9 + - - -
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Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU 2.9 19.6 + - - +
79A LEU* 3.2 7.8 + - - +
81A THR* 1.3 74.5 - - - +
83A ILE* 1.3 60.7 + - - +
85A SER* 3.2 7.9 + - - -
86A GLN* 2.9 27.7 + - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU 2.9 15.2 + - - +
80A HIS* 3.9 6.7 - - - +
82A ASP* 1.3 76.3 - - - +
84A VAL* 1.3 57.8 + - - +
86A GLN* 3.7 7.4 - - - +
87A LEU* 2.9 30.1 + - - +
130A ILE* 5.8 5.8 - - + -
111D GLU* 5.5 12.5 - - + +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A HIS 2.9 18.6 + - - +
81A THR* 3.7 8.1 - - - +
82A ASP 3.2 0.2 - - - -
83A ILE* 1.3 75.0 - - - +
85A SER* 1.3 57.2 + - - +
87A LEU* 3.5 6.2 + - - +
88A ASN* 2.9 28.9 + - - +
126A LEU* 5.9 8.7 - - + -
127A LEU* 5.9 9.2 - - + +
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A THR 2.9 18.1 + - - -
82A ASP* 3.5 7.2 - - - -
84A VAL* 1.3 75.6 - - - +
86A GLN* 1.3 60.0 + - - +
88A ASN* 3.2 7.6 + - - +
89A ASP* 2.9 28.8 + - - +
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ASP 2.9 15.8 + - - +
83A ILE* 3.3 8.3 + - - +
85A SER* 1.3 76.3 - - - +
87A LEU* 1.3 60.9 + - - +
89A ASP* 3.3 19.2 + - - +
90A LYS* 3.8 7.1 + - - +
111D GLU* 5.4 12.8 - - + +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE 2.9 18.2 + - - +
84A VAL* 3.9 6.5 - - - +
86A GLN* 1.3 75.3 - - - +
88A ASN* 1.3 58.6 + - - +
90A LYS* 3.1 25.1 + - - +
93A VAL* 5.3 3.0 - - + +
94A ARG* 3.7 16.6 + - + +
126A LEU* 6.1 4.7 - - + -
111D GLU* 5.8 7.1 - - + +
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Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL 2.9 20.1 + - - +
85A SER* 3.2 8.7 + - - +
87A LEU* 1.3 74.5 - - - +
89A ASP* 1.3 63.4 + - - +
90A LYS 3.2 5.3 + - - -
91A PRO* 4.7 2.4 - - - +
94A ARG* 5.2 3.8 - - - -
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER 2.9 12.2 + - - +
86A GLN* 3.6 13.9 - - - +
87A LEU 3.3 0.8 - - - -
88A ASN* 1.3 77.7 - - - +
90A LYS* 1.3 57.1 + - - +
91A PRO 4.0 1.8 - - - -
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN 3.8 5.5 + - - +
87A LEU* 3.1 18.8 + - - +
88A ASN 4.3 2.0 - - - +
89A ASP* 1.3 78.5 - - - +
91A PRO* 1.3 63.9 - - - +
92A GLU* 3.3 1.6 - - + +
93A VAL* 4.2 19.1 - - + +
94A ARG* 3.4 11.4 + - - +
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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