Contacts of the helix formed by residues 60 - 70 (chain C) in PDB entry 2VWI
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 LEU 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ILE* 6.0 0.4 - - + -
50C LEU* 3.9 15.7 - - + -
55C THR* 3.6 22.2 - - + +
56C SER 3.1 16.6 + - - +
57C MET* 3.2 7.3 + - - +
59C GLU* 1.3 75.4 - - - +
61C LEU* 1.3 64.4 + - - +
62C LYS 3.5 1.3 - - - -
63C GLU* 3.3 9.2 + - + +
64C ILE* 3.0 35.2 + - + +
88C LEU* 3.8 25.6 - - + -
167C VAL* 4.0 25.8 - - + -
170C PHE* 3.7 31.6 - - + -
171C LEU* 4.1 6.5 - - + -
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Residues in contact with LEU 61 (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 MET* 3.1 19.6 + - + +
58C ASP* 3.4 37.7 - - - +
59C GLU 3.4 2.4 - - - -
60C LEU* 1.3 77.2 - - - +
62C LYS* 1.3 59.5 + - - +
64C ILE* 3.3 8.6 + - + +
65C GLN* 3.1 27.0 + - - +
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Residues in contact with LYS 62 (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 GLU 4.6 11.8 + - - +
61C LEU* 1.3 77.0 - - - +
63C GLU* 1.3 77.6 + - + +
65C GLN* 3.8 13.2 - - - +
66C ALA* 3.0 28.2 + - - +
170C PHE* 4.7 2.0 - - - -
176C ASP* 2.7 37.4 + - - -
180C ASN* 3.3 31.6 - - + +
181C LYS* 4.3 5.3 + - - +
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Residues in contact with GLU 63 (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 GLU 4.9 0.7 - - - +
60C LEU* 3.3 15.5 + - - +
61C LEU 3.2 0.6 - - - -
62C LYS* 1.3 92.4 - - + +
64C ILE* 1.3 60.4 + - - +
66C ALA* 3.4 8.0 + - - +
67C MET* 3.0 33.4 + - - +
145C ARG* 5.0 5.9 + - - -
165C PHE* 5.9 1.2 - - - -
166C GLY* 3.5 23.6 - - - +
167C VAL* 4.0 18.4 - - + +
170C PHE* 3.5 44.6 - - + +
176C ASP* 4.9 0.3 - - - +
180C ASN* 5.8 2.4 - - - +
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Residues in contact with ILE 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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57C MET* 3.9 28.5 - - + -
60C LEU* 3.0 32.2 + - + +
61C LEU* 3.7 9.6 - - + +
63C GLU* 1.3 74.8 - - - +
65C GLN* 1.3 57.5 + - - +
67C MET* 3.3 11.5 + - - +
68C SER* 2.9 34.9 + - - +
78C TYR* 3.6 10.1 - - + +
81C SER* 3.5 23.8 - - - +
88C LEU* 4.2 12.1 - - + -
90C LEU* 5.0 2.7 - - + -
167C VAL* 3.7 15.5 - - + -
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Residues in contact with GLN 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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61C LEU 3.1 15.7 + - - +
62C LYS* 3.8 13.4 - - - +
63C GLU 3.3 0.2 - - - -
64C ILE* 1.3 78.4 - - - +
66C ALA* 1.3 60.5 + - - +
68C SER* 3.1 18.1 + - - -
69C GLN* 3.2 40.9 + - + +
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Residues in contact with ALA 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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1293A AU 3.4 10.3 - - - -
62C LYS 3.0 19.1 + - - +
63C GLU* 3.4 9.8 + - - +
65C GLN* 1.3 74.3 - - - +
67C MET* 1.3 58.3 + - - +
69C GLN* 3.1 5.2 + - - +
70C CYS* 2.9 31.0 + - - +
142C GLN* 3.7 33.4 - - - +
165C PHE* 3.9 11.2 - - + -
166C GLY* 6.0 0.2 - - - -
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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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63C GLU 3.0 17.7 + - - +
64C ILE* 3.3 13.7 + - - +
66C ALA* 1.3 76.2 - - - +
68C SER* 1.3 62.0 + - - +
69C GLN 3.4 0.5 + - - -
70C CYS 4.0 6.6 + - - +
71C HIS* 3.7 10.2 - - - -
78C TYR* 3.3 54.3 - - + +
90C LEU* 4.0 25.8 - - + -
165C PHE* 3.4 33.9 - - + +
166C GLY* 3.8 4.9 - - - -
167C VAL* 3.5 33.7 - - - +
168C SER 5.7 0.2 - - - +
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Residues in contact with SER 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 ILE* 2.9 18.2 + - - +
65C GLN* 3.1 15.4 + - - -
67C MET* 1.3 76.2 - - - +
69C GLN* 1.3 57.7 + - - +
71C HIS* 2.8 21.3 + - - -
78C TYR* 3.4 21.9 + - - -
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Residues in contact with GLN 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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1293A AU 4.0 12.0 - - - -
65C GLN* 3.3 37.6 + - + +
66C ALA* 3.1 6.3 + - - +
68C SER* 1.3 83.3 - - - +
70C CYS* 1.3 60.7 + - - +
71C HIS* 3.4 15.2 + - - -
136C TYR* 3.5 6.9 + - - -
140C ASN* 5.3 0.2 - - - +
142C GLN* 5.9 1.4 - - - +
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Residues in contact with CYS 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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1293A AU 2.0 33.4 - - - -
66C ALA 2.9 13.3 + - - +
67C MET 4.0 5.6 + - - +
68C SER 3.8 0.4 - - - -
69C GLN* 1.3 74.3 - - - +
71C HIS* 1.3 65.9 + - - +
75C ILE* 4.3 14.5 - - - +
78C TYR* 6.0 0.7 - - - +
136C TYR* 3.4 13.5 - - + -
137C LEU* 3.9 14.6 - - + -
140C ASN* 4.0 17.3 - - - -
142C GLN* 3.8 18.6 - - - -
165C PHE* 3.8 15.9 - - + -
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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