Contacts of the helix formed by residues 56 - 70 (chain A) in PDB entry 2QY7
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 GLN 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLU* 4.9 14.2 + - - +
24A ILE* 3.6 29.7 + - + +
50A ALA* 3.6 20.8 - - + +
53A MET* 3.0 44.9 + - + +
55A GLU* 1.3 84.6 - - + +
57A PHE* 1.3 64.8 + - - +
58A PRO* 3.3 3.9 - - - -
59A GLU* 3.4 8.7 + - - +
60A LEU* 3.0 23.3 + - - +
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Residues in contact with PHE 57 (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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50A ALA 4.7 3.1 - - - -
51A THR* 3.6 27.4 - - + +
53A MET 3.0 11.9 + - - +
54A TYR 4.3 0.2 - - - +
56A GLN* 1.3 76.1 - - - +
58A PRO* 1.4 65.6 - - + +
60A LEU* 3.3 5.7 + - + +
61A MET* 2.8 59.4 + - + +
96A ARG* 3.5 78.5 - - + +
97A VAL* 3.8 20.2 - - + -
100A SER* 4.3 7.4 - - - -
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Residues in contact with PRO 58 (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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54A TYR 3.4 17.9 - - - +
55A GLU 4.3 5.6 - - - +
56A GLN 3.5 4.3 - - - -
57A PHE* 1.4 99.5 - - + +
59A GLU* 1.3 57.8 + - + +
61A MET* 3.9 2.0 - - + -
62A ASN* 2.8 50.8 + - - +
96A ARG* 5.1 5.6 - - - +
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Residues in contact with GLU 59 (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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22A SER* 3.6 24.7 + - - -
24A ILE* 4.3 8.1 - - + +
25A GLU* 4.0 31.7 - - + +
55A GLU 4.2 13.0 - - - +
56A GLN* 3.4 7.4 + - - +
58A PRO* 1.3 80.3 - - + +
60A LEU* 1.3 62.5 + - - +
62A ASN* 4.3 3.7 - - - +
63A MET* 3.0 26.9 + - - +
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Residues in contact with LEU 60 (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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24A ILE* 3.5 34.2 - - + +
28A VAL* 3.9 11.4 - - + +
47A ILE* 3.5 40.8 - - + +
50A ALA* 3.8 7.2 - - + +
51A THR* 3.6 33.0 - - + +
56A GLN 3.0 17.0 + - - +
57A PHE* 3.4 5.4 - - - +
59A GLU* 1.3 78.9 - - - +
61A MET* 1.3 72.7 + - + +
63A MET* 3.7 3.0 - - - +
64A LEU* 3.1 21.1 + - + +
89A LEU* 4.1 10.5 - - + -
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Residues in contact with MET 61 (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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57A PHE* 2.8 59.6 + - + +
58A PRO* 4.1 2.7 - - + +
60A LEU* 1.3 87.3 - - + +
62A ASN* 1.3 59.4 + - - +
64A LEU* 3.2 16.4 + - + +
65A TRP* 2.9 70.3 + - + +
86A LEU* 4.4 15.5 - - + -
89A LEU* 4.6 1.8 - - - -
97A VAL* 4.2 15.7 - - + -
100A SER* 3.7 16.8 - - - +
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Residues in contact with ASN 62 (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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58A PRO* 2.8 40.5 + - - +
59A GLU* 4.3 3.1 - - - +
61A MET* 1.3 72.9 - - - +
63A MET* 1.3 59.6 + - - +
65A TRP* 4.0 12.0 - - - +
66A SER* 3.0 29.5 + - - -
70A LYS* 5.7 0.5 + - - -
104A HIS* 5.6 3.1 + - - -
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Residues in contact with MET 63 (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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21A TYR* 3.7 32.8 - - + +
25A GLU* 3.6 36.3 + - + +
28A VAL* 3.7 15.5 - - + -
29A ARG* 3.7 36.1 - - + +
59A GLU 3.0 20.0 + - - +
60A LEU 3.7 3.6 - - - +
62A ASN* 1.3 75.0 - - - +
64A LEU* 1.3 65.3 + - - +
66A SER* 3.3 10.6 + - - -
67A ARG* 2.9 40.3 + - + +
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Residues in contact with LEU 64 (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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28A VAL* 3.6 13.4 - - + +
32A THR* 6.1 0.2 - - - -
60A LEU* 3.1 15.3 + - + +
61A MET* 3.2 20.6 + - + +
63A MET* 1.3 77.7 - - - +
65A TRP* 1.3 75.5 + - + +
67A ARG* 3.3 3.9 + - - +
68A MET* 3.1 51.1 + - + +
82A SER* 4.2 9.5 - - - +
85A LEU* 4.0 20.0 - - + -
86A LEU* 4.2 17.7 - - + +
89A LEU* 3.8 28.7 - - + -
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Residues in contact with TRP 65 (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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61A MET* 2.9 47.4 + - + +
62A ASN* 4.1 11.7 - - - +
64A LEU* 1.3 76.2 - - + +
66A SER* 1.3 61.8 + - - +
68A MET* 3.8 27.8 - - + -
69A LEU* 2.9 58.3 + - + +
70A LYS* 5.5 1.5 - - - +
86A LEU* 3.8 19.7 - - + -
100A SER* 3.1 30.5 + - - -
101A ALA* 4.0 10.5 - - - -
104A HIS* 3.7 50.9 + + + -
108A LEU* 3.9 17.5 - - + -
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Residues in contact with SER 66 (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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62A ASN 3.0 19.8 + - - -
63A MET* 3.5 15.2 - - - -
65A TRP* 1.3 77.5 - - - +
67A ARG* 1.3 57.2 + - - +
70A LYS* 2.9 61.8 + - - +
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Residues in contact with ARG 67 (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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28A VAL* 4.9 1.6 - - + -
29A ARG* 3.0 67.2 + - + +
32A THR* 2.9 42.4 + - + +
33A ASN* 3.8 7.3 - - - +
34A ASP* 6.0 0.4 + - - -
63A MET* 2.9 37.6 + - + +
64A LEU* 3.9 3.8 - - - +
66A SER* 1.3 76.7 - - - +
68A MET* 1.3 61.1 + - - +
70A LYS 4.8 0.5 - - - +
72A ASN* 4.5 3.3 - - - +
78A ARG* 3.4 62.6 + - + +
79A VAL* 4.3 5.4 - - - +
82A SER* 4.6 1.8 - - - -
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Residues in contact with MET 68 (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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64A LEU* 3.1 37.1 + - + +
65A TRP* 3.8 22.7 - - + +
66A SER 3.2 0.2 - - - -
67A ARG* 1.3 78.5 - - - +
69A LEU* 1.3 58.5 + - + +
72A ASN* 2.8 24.4 - - - +
79A VAL* 3.5 18.6 - - + +
82A SER* 3.0 37.2 + - - +
83A LEU* 3.7 17.5 - - + -
86A LEU* 4.0 7.6 - - + -
108A LEU* 3.7 22.0 - - - -
111A LEU* 3.7 22.2 - - + +
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Residues in contact with LEU 69 (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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65A TRP* 2.9 42.0 + - + +
68A MET* 1.3 82.3 - - + +
70A LYS* 1.3 68.5 + - + +
71A ASP 3.9 1.0 + - - -
72A ASN* 3.7 14.5 + - - +
104A HIS* 5.5 0.9 - - - +
107A ASP* 3.8 44.4 - - + +
110A SER* 4.5 4.3 - - - +
111A LEU* 3.8 35.0 - - + -
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Residues in contact with LYS 70 (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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62A ASN 5.7 0.2 + - - -
65A TRP 5.8 1.1 - - - -
66A SER* 2.9 44.1 + - - +
67A ARG 4.8 1.2 - - - +
68A MET 3.8 0.2 - - - -
69A LEU* 1.3 81.3 - - + +
71A ASP* 1.3 77.3 + - - +
72A ASN* 3.2 5.0 + - - +
78A ARG* 4.2 6.8 + - - -
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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