Contacts of the helix formed by residues 63 - 72 (chain C) in PDB entry 2VUU
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 ASN 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C GLY* 4.8 1.2 - - - -
59C PRO* 3.0 48.0 + - + +
60C LEU 3.4 4.2 + - - +
61C LEU 3.2 2.6 - - - +
62C ASN* 1.3 77.8 - - - +
64C VAL* 1.3 59.7 + - - +
65C PRO* 3.1 20.3 - - - +
66C LEU* 3.2 26.7 + - - +
67C MET* 3.0 27.7 + - - +
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Residues in contact with VAL 64 (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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62C ASN* 3.9 3.0 - - - -
63C ASN* 1.3 73.4 - - - +
65C PRO* 1.3 74.6 - - + +
66C LEU 3.2 0.7 - - - -
67C MET* 3.8 18.8 - - + -
68C ASP* 3.0 30.8 + - - +
94C ASP* 4.2 19.3 - - + +
101C ARG* 3.2 31.0 - - - +
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Residues in contact with PRO 65 (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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62C ASN 5.2 1.1 - - - +
63C ASN* 3.1 15.3 - - - +
64C VAL* 1.3 95.2 - - + +
66C LEU* 1.3 61.3 + - - +
68C ASP* 3.4 6.9 + - + +
69C THR* 3.1 26.7 + - - -
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Residues in contact with LEU 66 (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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35C GLN* 4.0 26.9 - - + -
56C PHE* 4.6 16.6 - - + +
57C GLN 4.9 1.1 - - - -
58C GLY* 3.8 26.0 - - - +
59C PRO 3.6 20.4 - - - +
60C LEU* 4.4 8.1 - - + -
63C ASN* 3.2 26.9 + - + +
65C PRO* 1.3 80.3 - - - +
67C MET* 1.3 62.4 + - + +
69C THR* 3.1 8.2 + - - -
70C LEU* 2.9 37.5 + - + -
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Residues in contact with MET 67 (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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60C LEU* 3.1 34.1 - - + +
63C ASN 3.0 30.5 + - - +
64C VAL* 3.4 13.4 + - + +
65C PRO 3.3 0.4 - - - -
66C LEU* 1.3 81.8 - - + +
68C ASP* 1.3 60.3 + - - +
70C LEU* 3.4 4.8 + - + +
71C PHE* 2.8 33.3 + - + -
91C ILE* 4.4 2.5 - - - +
94C ASP* 3.4 40.8 - - + +
95C LEU* 3.4 36.8 - - + -
98C ALA* 3.7 15.3 - - + -
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Residues in contact with ASP 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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64C VAL* 3.0 30.9 + - - +
65C PRO* 3.8 6.3 - - + +
66C LEU 3.3 0.2 - - - -
67C MET* 1.3 72.6 - - - +
69C THR* 1.3 68.4 + - - +
71C PHE* 3.5 5.5 + - - +
72C GLU* 3.3 23.5 + - - +
98C ALA* 4.0 10.3 - - - +
101C ARG* 3.2 34.6 + - - +
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Residues in contact with THR 69 (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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33C ARG* 3.0 35.1 + - - +
56C PHE* 3.7 24.7 - - + -
65C PRO 3.1 15.0 + - - -
66C LEU* 3.1 10.2 + - - -
68C ASP* 1.3 76.5 - - - +
70C LEU* 1.3 64.3 + - - +
72C GLU* 3.0 28.1 + - - +
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Residues in contact with LEU 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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9C ALA* 3.7 17.2 - - + +
10C VAL 3.6 11.0 - - - +
11C VAL* 3.6 31.0 - - + -
33C ARG* 3.1 66.2 + - + +
34C ALA* 3.8 6.1 - - - +
35C GLN* 4.0 5.4 - - + +
56C PHE* 3.9 15.0 - - + -
66C LEU* 2.9 24.0 + - + +
67C MET* 3.6 5.4 - - - +
68C ASP 3.3 0.2 - - - -
69C THR* 1.3 77.5 - - - +
71C PHE* 1.3 71.0 + - + +
74C ALA* 4.3 0.2 - - - +
79C ILE* 5.2 0.7 - - + -
95C LEU* 5.1 2.9 - - + -
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Residues in contact with PHE 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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9C ALA* 4.0 21.3 - - + -
67C MET* 2.8 28.1 + - + +
68C ASP* 4.0 5.4 - - - +
69C THR 3.2 0.8 - - - -
70C LEU* 1.3 81.3 - - + +
72C GLU* 1.3 63.7 + - - +
73C GLY 3.1 1.4 + - - -
74C ALA* 3.1 17.2 + - - +
77C ALA* 4.2 15.5 - - + -
79C ILE* 4.7 8.3 - - + -
95C LEU* 3.4 33.2 - - + -
98C ALA* 3.2 31.4 - - + +
99C ALA* 3.6 23.6 - - + -
102C ALA* 3.7 28.4 - - + +
104C THR* 3.9 1.9 + - - -
105C ILE* 4.0 11.0 - - + -
108C TYR* 4.4 5.4 - + - -
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Residues in contact with GLU 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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33C ARG* 3.2 32.8 + - - +
68C ASP 3.3 12.3 + - - +
69C THR* 3.0 35.5 + - - +
71C PHE* 1.3 75.7 - - - +
73C GLY* 1.3 61.2 + - - +
74C ALA 3.3 1.2 + - - -
102C ALA* 5.6 0.9 - - - -
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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