Contacts of the helix formed by residues 67 - 76 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LYS* 5.9 0.2 - - + -
52C THR 3.7 13.9 - - - -
53C PRO* 3.2 20.7 + - + +
55C ASP* 3.1 38.0 + - + -
56C SER 4.5 3.8 - - - -
57C PHE* 3.6 34.1 - + + -
66C THR* 1.3 72.5 - - - +
68C LEU* 1.3 61.9 + - - +
70C TYR* 3.2 6.5 + - - +
71C TYR* 3.1 48.3 + + + -
79C VAL* 5.3 0.4 - - - -
86C LEU* 3.8 27.1 - - + -
107C LEU* 4.0 25.1 - - + -
109C LEU* 4.6 7.4 - - + -
60D SER* 4.1 17.7 - - - -
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PRO* 3.3 29.5 + - + +
54C LYS* 4.3 14.4 - - + -
66C THR* 3.5 9.6 - - + +
67C PHE* 1.3 77.4 - - - +
69C GLU* 1.4 54.1 + - - +
71C TYR* 3.6 2.3 + - - +
72C SER* 2.7 31.4 + - - -
77C ILE 4.7 1.2 - - - +
78C THR* 6.1 0.2 - - - -
79C VAL* 3.8 35.2 + - + +
82C GLU* 3.9 39.0 - - + +
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 5.0 7.0 - - + -
66C THR* 3.2 22.3 + - - +
68C LEU* 1.4 75.6 - - - +
70C TYR* 1.3 59.8 + - - +
72C SER* 3.2 7.2 + - - -
73C LYS* 3.0 35.0 + - - +
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Residues in contact with TYR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PHE* 3.4 28.0 - + + -
59C MET* 5.2 4.7 - - + -
65C ILE* 5.1 5.8 - - + +
66C THR 3.0 12.9 + - - +
67C PHE* 3.2 8.5 + - - +
69C GLU* 1.3 76.7 - - - +
71C TYR* 1.3 78.7 + + - +
73C LYS* 5.0 0.4 - - - -
74C ASN* 2.8 60.9 + - - +
75C TYR* 3.9 9.9 + + - -
59D MET* 3.4 38.0 - - + +
60D SER* 3.7 13.2 - - - -
61D ASP* 2.3 43.7 + - - -
63D LYS* 3.6 10.0 - - - +
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Residues in contact with TYR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TYR* 3.5 24.2 + + - -
67C PHE* 3.1 39.4 + + + +
68C LEU 4.3 0.4 - - - +
70C TYR* 1.3 88.6 - + - +
72C SER* 1.3 60.5 + - - +
75C TYR* 3.0 48.9 + + - +
76C GLY 3.3 5.7 + - - -
77C ILE* 3.3 20.7 + - + +
79C VAL* 4.1 11.9 - - + -
107C LEU 3.7 11.6 + - - -
108C LEU* 4.5 3.5 - - - -
109C LEU* 3.7 38.5 + - + +
112C LEU* 3.6 21.8 - - + -
60D SER* 4.8 1.2 + - - -
61D ASP* 3.4 20.4 - - - +
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Residues in contact with SER 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU 2.7 24.1 + - - -
69C GLU* 3.2 14.7 + - - -
71C TYR* 1.3 75.4 - - - +
73C LYS* 1.4 55.0 + - - +
76C GLY* 3.1 24.9 + - - -
77C ILE 3.2 19.0 + - - +
78C THR* 5.3 6.1 - - - -
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Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLU 3.0 19.3 + - - +
70C TYR* 4.3 1.3 - - - +
72C SER* 1.4 76.7 + - - +
74C ASN* 1.4 65.9 + - - +
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Residues in contact with ASN 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C MET* 6.2 0.4 - - - +
70C TYR* 2.8 58.0 + - - +
73C LYS* 1.4 85.0 - - - +
75C TYR* 1.3 84.8 + - + +
76C GLY 3.9 0.2 - - - -
59D MET* 3.9 18.0 - - - +
63D LYS* 3.9 15.5 - - + +
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Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TYR* 3.5 35.9 - + + -
38C ASN* 5.2 7.4 + - + -
70C TYR* 4.0 6.7 - + - -
71C TYR* 3.0 35.9 + + - +
74C ASN* 1.3 94.5 - - + +
76C GLY* 1.3 62.5 + - - +
77C ILE* 3.5 21.6 + - + +
61D ASP* 2.5 37.0 + - - -
63D LYS* 3.6 30.8 - - + +
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C SER* 3.1 20.6 + - - -
73C LYS 4.8 0.2 - - - -
74C ASN 3.9 0.4 - - - -
75C TYR* 1.3 76.6 - - - +
77C ILE* 1.3 59.4 + - - +
78C THR* 4.1 4.1 + - - -
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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