Contacts of the helix formed by residues 78 - 90 (chain C) in PDB entry 2QXU
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 MET 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C GLY* 3.9 2.4 - - - -
12C ILE* 3.4 52.9 - - + +
45C THR 4.5 4.5 - - - +
46C GLY* 3.4 26.9 - - - +
47C THR* 6.1 0.7 - - - -
48C ASN* 5.4 1.6 - - - +
76C HIS 3.2 0.2 + - - -
77C SER* 1.3 81.4 + - - +
79C GLY* 1.3 63.1 + - - +
81C ALA* 3.0 22.2 + - - +
82C ASN* 3.0 14.2 + - - +
105C ALA* 4.4 5.6 - - + +
108C LEU* 3.6 33.4 - - + -
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Residues in contact with GLY 79 (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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9C VAL* 3.7 15.4 - - - +
10C HIS 3.4 20.6 + - - -
75C ALA* 3.5 6.9 - - - +
76C HIS 2.8 14.6 + - - -
78C MET* 1.3 79.8 - - - +
80C GLY* 1.3 54.9 + - - +
82C ASN* 3.7 5.4 - - - +
83C THR* 2.8 33.6 + - - -
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Residues in contact with GLY 80 (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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75C ALA* 3.7 15.1 - - - +
76C HIS 4.0 1.0 + - - -
77C SER 2.9 10.7 + - - -
79C GLY* 1.3 76.6 - - - +
81C ALA* 1.3 63.2 + - - +
83C THR* 3.3 3.6 + - - -
84C LEU* 3.0 28.1 + - - +
101C THR* 4.2 7.0 - - - +
104C GLY* 4.7 1.8 - - - -
106C ASN* 3.3 22.4 - - - -
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Residues in contact with ALA 81 (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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48C ASN* 3.3 11.8 - - - +
77C SER 4.0 2.0 + - - -
78C MET* 3.0 26.0 + - - +
80C GLY* 1.3 76.8 - - - +
82C ASN* 1.3 61.4 + - - +
84C LEU* 3.3 1.3 + - - -
85C TYR 3.0 14.4 + - - -
105C ALA 3.4 22.5 + - - +
106C ASN* 4.0 4.2 + - - +
108C LEU* 4.1 6.3 - - + -
109C THR* 2.9 31.4 + - - +
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Residues in contact with ASN 82 (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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9C VAL* 4.7 5.8 - - + -
10C HIS 4.5 1.6 + - - -
11C GLY* 5.7 0.4 - - - -
41C PHE* 3.9 11.0 - - + -
46C GLY 3.0 18.5 + - - +
48C ASN* 2.8 28.6 - - - +
51C ASN* 2.9 47.4 - - + +
52C GLY* 4.7 2.8 - - - +
55C LEU* 4.1 7.9 - - + +
78C MET* 3.0 17.1 + - - +
79C GLY* 3.7 12.0 - - - +
81C ALA* 1.3 74.4 - - - +
83C THR* 1.3 63.8 + - - +
85C TYR* 3.2 5.4 + - - +
86C TYR* 3.0 23.6 + - - +
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Residues in contact with THR 83 (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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9C VAL* 3.9 8.7 - - - +
55C LEU* 3.9 9.6 - - - +
73C ILE* 3.7 36.6 - - + +
75C ALA* 3.5 12.2 - - - +
79C GLY 2.8 22.9 + - - -
80C GLY* 3.5 7.2 - - - -
81C ALA 3.2 0.2 - - - -
82C ASN* 1.3 76.1 - - - +
84C LEU* 1.3 66.0 + - + +
86C TYR* 3.2 5.5 + - - +
87C ILE* 3.1 34.9 + - + +
99C VAL* 4.3 15.9 - - + -
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Residues in contact with LEU 84 (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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80C GLY 3.0 18.5 + - - +
81C ALA 3.3 3.6 + - - +
83C THR* 1.3 79.8 - - + +
85C TYR* 1.3 53.0 + - - +
87C ILE* 3.4 4.8 + - + +
88C LYS* 2.8 36.9 + - - +
106C ASN* 3.4 46.0 - - + +
109C THR* 3.8 6.3 - - + -
110C THR* 3.8 28.5 - - + -
112C LYS 4.2 5.6 - - - +
114C LEU* 4.0 5.6 - - + +
125C TYR* 3.8 34.5 - - + +
143C LEU* 3.9 14.4 - - + -
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Residues in contact with TYR 85 (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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48C ASN* 3.6 52.5 - - + +
49C TYR* 4.5 15.5 - - - -
52C GLY* 3.9 10.1 - - - -
53C PRO* 4.8 3.6 - - + -
81C ALA 3.0 13.5 + - - +
82C ASN* 3.4 8.5 - - - +
84C LEU* 1.3 74.2 - - - +
86C TYR* 1.3 60.7 + - - +
88C LYS* 4.4 1.8 - - - -
89C ASN* 2.8 59.4 + - + +
90C LEU* 3.5 26.6 + - + +
109C THR* 3.5 11.8 - - + +
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Residues in contact with TYR 86 (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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52C GLY* 4.7 2.9 - - - +
55C LEU* 3.9 22.7 - - + -
56C SER* 3.4 36.8 + - - -
59C VAL* 3.2 42.6 - - + +
73C ILE* 4.6 4.7 - - + -
82C ASN 3.0 12.2 + - - +
83C THR 3.3 10.8 - - - +
85C TYR* 1.3 77.9 - - - +
87C ILE* 1.3 61.8 + - + +
90C LEU* 3.1 35.6 + - + +
91C ASP* 3.8 6.4 + - - -
92C GLY* 3.1 45.5 + - - -
95C LYS* 3.7 18.5 - - - +
96C VAL* 3.9 16.2 - - + -
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Residues in contact with ILE 87 (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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83C THR* 3.1 29.1 + - + +
84C LEU* 3.7 9.0 - - - +
86C TYR* 1.3 87.0 - - + +
88C LYS* 1.3 60.6 + - - +
90C LEU 4.4 3.8 - - - +
92C GLY* 4.0 20.0 - - - +
93C GLY* 4.0 16.6 + - - -
96C VAL* 4.4 6.7 - - + -
99C VAL* 4.2 14.4 - - + -
114C LEU* 3.9 24.0 - - + -
116C GLY* 5.1 2.5 - - - +
123C ILE* 3.8 26.7 - - + -
125C TYR* 3.6 18.4 - - + +
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Residues in contact with LYS 88 (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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84C LEU 2.8 21.4 + - - +
85C TYR* 4.0 1.6 - - - +
87C ILE* 1.3 77.6 - - - +
89C ASN* 1.3 85.1 + - - +
90C LEU 5.0 0.6 - - - +
109C THR* 4.2 26.9 - - + +
110C THR* 4.4 6.7 + - - +
114C LEU* 3.2 25.3 - - + +
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Residues in contact with ASN 89 (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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85C TYR* 2.8 53.9 + - + +
88C LYS* 1.3 111.3 + - - +
90C LEU* 1.3 69.4 + - + +
109C THR* 5.2 0.2 - - - +
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Residues in contact with LEU 90 (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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52C GLY* 3.3 42.4 - - - +
53C PRO* 3.6 12.1 - - + -
56C SER* 4.3 6.3 - - - -
85C TYR* 4.2 18.2 - - + +
86C TYR* 3.1 29.4 + - + +
87C ILE 4.4 5.5 - - - +
88C LYS 5.0 0.5 - - - -
89C ASN* 1.3 89.0 - - + +
91C ASP* 1.3 68.6 + - - +
92C GLY 3.5 2.3 + - - -
93C GLY 4.7 1.0 + - - -
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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