Contacts of the helix formed by residues 67 - 76 (chain A) in PDB entry 3QIR
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 PHE 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LYS* 5.6 1.8 - - + -
52A THR 3.6 16.4 - - - -
53A PRO* 3.3 20.2 + - + +
55A ASP* 3.1 36.0 + - + -
56A SER 4.5 3.8 - - - -
57A PHE* 3.5 35.0 - + + -
66A THR* 1.3 69.1 - - - +
68A LEU* 1.4 65.3 + - - +
70A TYR* 3.9 5.6 - - - -
71A TYR* 2.9 50.6 + + + -
79A VAL* 5.3 0.4 - - - -
86A LEU* 3.6 30.5 - - + -
107A LEU* 4.1 18.6 - - + -
109A LEU* 4.7 7.2 - - + -
60B SER* 3.9 20.6 - - - -
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Residues in contact with LEU 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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53A PRO* 3.2 26.5 + - + +
54A LYS* 4.3 17.7 - - + -
66A THR* 3.2 8.9 - - + +
67A PHE* 1.4 77.5 - - - +
69A GLU* 1.4 60.8 + - - +
71A TYR* 3.6 1.7 + - - +
72A SER* 3.2 23.0 + - - -
77A ILE 4.7 1.2 - - - +
79A VAL* 3.7 35.0 + - + +
82A GLU* 3.9 39.9 - - + +
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Residues in contact with GLU 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 ILE* 3.8 16.2 - - + -
66A THR* 3.0 22.4 + - + +
68A LEU* 1.4 72.3 - - - +
70A TYR* 1.3 59.6 + - - +
72A SER* 4.1 5.1 - - - -
73A LYS* 3.0 35.3 + - + +
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Residues in contact with TYR 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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57A PHE* 3.5 25.6 - + + -
59A MET* 5.4 2.9 - - - -
65A ILE* 4.0 12.0 - - + +
66A THR 2.9 14.3 + - - +
67A PHE* 3.2 11.9 + - - +
69A GLU* 1.3 75.7 - - - +
71A TYR* 1.3 78.0 + + - +
73A LYS* 4.4 1.5 - - - +
74A ASN* 3.0 62.7 + - - +
75A TYR* 3.9 10.6 + + - -
59B MET* 3.5 31.6 - - + +
60B SER* 4.0 11.0 - - - -
61B ASP* 2.6 39.1 + - - -
63B LYS* 3.5 11.4 - - - +
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Residues in contact with TYR 71 (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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37A TYR* 3.4 31.8 + + - -
67A PHE* 2.9 44.9 + + + +
68A LEU 4.3 0.2 - - - +
70A TYR* 1.3 87.6 - + - +
72A SER* 1.3 56.5 + - - +
75A TYR* 3.0 48.7 + + - +
76A GLY 3.3 5.7 + - - -
77A ILE* 3.3 23.1 + - + +
79A VAL* 4.1 14.1 - - + -
107A LEU 3.9 9.9 + - - -
108A LEU* 4.6 0.5 - - - -
109A LEU* 3.7 41.3 + - + +
112A LEU* 5.0 6.1 - - + -
60B SER* 4.5 1.4 + - - -
61B ASP* 3.4 22.7 - - - +
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Residues in contact with SER 72 (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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68A LEU 3.2 18.2 + - - -
69A GLU* 4.1 4.9 - - - -
70A TYR 3.4 0.2 - - - -
71A TYR* 1.3 77.3 - - - +
73A LYS* 1.3 58.3 + - - +
76A GLY* 3.1 24.7 + - - -
77A ILE 3.2 18.5 + - - +
78A THR* 5.3 5.6 - - - -
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Residues in contact with LYS 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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69A GLU* 3.0 19.7 + - + +
70A TYR* 4.4 1.6 - - - +
72A SER* 1.3 78.1 + - - +
74A ASN* 1.3 62.5 + - - +
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Residues in contact with ASN 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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70A TYR* 3.0 57.4 + - - +
73A LYS* 1.3 80.5 - - - +
75A TYR* 1.3 76.9 + - + +
59B MET* 3.7 15.5 - - - +
63B LYS* 3.7 19.1 - - - +
65B ILE* 6.0 1.0 - - - +
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Residues in contact with TYR 75 (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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37A TYR* 3.4 43.7 - + + -
38A ASN* 5.0 6.0 - - + +
70A TYR* 3.9 6.0 + + - -
71A TYR* 3.0 35.6 + + - +
74A ASN* 1.3 95.4 - - + +
76A GLY* 1.3 63.8 + - - +
77A ILE* 3.5 19.1 + - + +
61B ASP* 2.9 22.0 + - - -
63B LYS* 3.4 40.8 - - + +
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Residues in contact with GLY 76 (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 SER* 3.1 20.6 + - - -
73A LYS 4.8 0.2 - - - -
74A ASN 3.8 0.4 - - - -
75A TYR* 1.3 77.9 - - - +
77A ILE* 1.4 59.2 + - - +
78A THR* 4.0 5.2 + - - -
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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