Contacts of the helix formed by residues 67 - 76 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A SER* 3.9 18.2 - - - -
51B LYS* 5.5 1.8 - - + -
52B THR 3.7 14.4 - - - -
53B PRO* 3.2 20.0 + - + +
55B ASP* 3.1 35.9 + - + -
56B SER 4.4 4.3 - - - -
57B PHE* 3.6 33.4 - + + -
66B THR* 1.3 73.7 - - - +
68B LEU* 1.4 62.3 + - - +
70B TYR* 3.3 5.4 + - - +
71B TYR* 3.0 48.9 + + + -
79B VAL* 5.3 0.4 - - - -
86B LEU* 3.5 31.2 - - + -
107B LEU* 4.0 22.4 - - + -
109B LEU* 4.6 8.3 - - + -
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Residues in contact with LEU 68 (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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53B PRO* 3.2 29.2 + - + +
54B LYS* 4.3 12.8 - - + -
66B THR* 3.6 8.1 - - + +
67B PHE* 1.4 76.0 - - - +
69B GLU* 1.4 61.2 + - + +
71B TYR* 3.6 2.1 + - - +
72B SER* 3.3 24.1 + - - -
77B ILE 4.7 1.0 - - - +
79B VAL* 3.7 35.8 + - + +
82B GLU* 3.6 41.3 - - + +
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Residues in contact with GLU 69 (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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64B GLU 5.0 0.9 - - - +
65B ILE* 3.7 23.9 - - + +
66B THR* 3.0 35.2 + - - +
68B LEU* 1.4 72.8 - - + +
70B TYR* 1.3 59.9 + - - +
72B SER* 4.1 4.6 - - - -
73B LYS* 2.9 35.0 + - + +
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Residues in contact with TYR 70 (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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59A MET* 3.6 29.8 - - + +
60A SER* 4.0 10.8 - - - -
61A ASP* 2.5 40.7 + - - -
63A LYS* 3.5 18.2 - - - +
57B PHE* 3.5 28.7 - + + -
59B MET* 5.5 2.0 - - - -
65B ILE* 3.8 15.7 - - + +
66B THR 3.0 13.7 + - - +
67B PHE 3.3 8.3 + - - +
69B GLU* 1.3 76.9 - - - +
71B TYR* 1.3 78.5 + + - +
74B ASN* 3.0 58.0 + - - +
75B TYR* 3.8 11.6 + + - -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 4.7 1.6 + - - -
61A ASP* 3.3 26.1 - - - +
37B TYR* 3.4 24.6 + + - -
67B PHE* 3.0 39.8 + + + +
68B LEU 4.3 0.2 - - - +
70B TYR* 1.3 88.4 - + - +
72B SER* 1.3 60.6 + - - +
75B TYR* 3.0 43.1 + + - +
77B ILE* 3.3 27.2 + - + +
79B VAL* 4.1 11.7 - - + -
107B LEU 3.7 10.6 + - - -
108B LEU* 4.5 0.9 - - - -
109B LEU* 3.7 40.5 + - + +
112B LEU* 3.6 20.9 - - + -
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Residues in contact with SER 72 (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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68B LEU 3.3 16.7 + - - -
69B GLU* 4.1 4.3 - - - -
71B TYR* 1.3 76.2 - - - +
73B LYS* 1.4 58.8 + - - +
76B GLY* 3.1 24.5 + - - -
77B ILE 3.2 18.7 + - - +
78B THR* 5.2 6.7 - - - -
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Residues in contact with LYS 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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65B ILE* 5.3 5.4 - - + -
69B GLU 2.9 20.3 + - - +
70B TYR* 4.3 1.3 - - - +
72B SER* 1.4 77.1 - - - +
74B ASN* 1.4 65.6 + - - +
76B GLY 5.1 0.3 + - - -
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Residues in contact with ASN 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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59A MET* 4.1 10.9 - - - +
63A LYS* 3.1 39.6 + - - +
65B ILE* 5.1 2.6 - - - +
70B TYR* 3.0 45.6 + - - +
73B LYS* 1.4 84.2 - - - +
75B TYR* 1.3 77.5 + - + +
76B GLY 3.9 0.2 - - - -
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Residues in contact with TYR 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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61A ASP* 2.7 34.5 + - - -
63A LYS* 3.6 35.7 - - + +
37B TYR* 3.4 31.9 - + + -
38B ASN* 4.2 10.9 + - + -
70B TYR* 4.0 6.3 - + - -
71B TYR* 3.0 35.4 + + - +
74B ASN* 1.3 90.8 - - + +
76B GLY* 1.3 62.6 + - - +
77B ILE* 3.5 21.4 + - + +
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Residues in contact with GLY 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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72B SER* 3.1 20.6 + - - -
73B LYS 4.8 0.2 - - - -
74B ASN 3.9 0.4 - - - -
75B TYR* 1.3 78.2 - - - +
77B ILE* 1.4 60.0 + - - +
78B THR* 4.0 4.4 + - - -
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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