Contacts of the helix formed by residues 60 - 71 (chain B) in PDB entry 2VDY
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 CYS 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B THR* 1.3 74.8 - - - +
61B GLY* 1.3 69.8 - - - +
62B HIS 3.6 0.7 + - - -
63B THR 3.6 0.3 + - - -
64B ARG* 3.4 17.1 + - - -
308B ASN* 3.3 42.9 + - - +
310B SER* 3.5 11.9 - - - +
311B ARG* 3.7 23.3 - - - -
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Residues in contact with GLY 61 (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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60B CYS* 1.3 79.5 - - - +
62B HIS* 1.3 57.1 + - - -
64B ARG* 3.3 6.6 + - - +
65B ALA* 3.1 26.5 + - - +
308B ASN* 4.9 4.5 - - - -
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Residues in contact with HIS 62 (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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60B CYS 3.6 0.6 + - - -
61B GLY* 1.3 70.3 - - - -
63B THR* 1.3 59.7 + - - +
65B ALA* 3.8 8.9 - - + -
66B GLN* 2.8 51.3 + - + +
301B ASP* 2.7 27.3 + - - +
308B ASN* 5.7 0.6 - - - +
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Residues in contact with THR 63 (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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59B THR* 4.2 6.9 + - + -
60B CYS 3.6 8.7 + - - -
61B GLY 3.4 0.4 - - - -
62B HIS* 1.3 76.3 - - - +
64B ARG* 1.3 62.3 + - - +
66B GLN* 4.1 0.9 - - - +
67B LEU* 3.2 25.6 + - - +
301B ASP* 3.7 31.9 + - + +
302B LEU* 3.8 28.9 - - + +
306B GLN 4.2 2.6 + - - -
307B ALA* 4.0 3.4 - - + -
308B ASN* 3.0 41.2 + - - +
309B PHE* 5.0 0.9 - - + -
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Residues in contact with ARG 64 (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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56B SER* 3.7 7.4 - - - +
59B THR* 3.2 34.9 + - - +
60B CYS* 3.4 19.5 + - - +
61B GLY 3.3 11.5 + - - +
62B HIS 3.2 0.2 - - - -
63B THR* 1.3 78.9 - - - +
65B ALA* 1.3 61.9 + - - +
67B LEU* 3.5 2.0 + - - +
68B LEU* 3.2 46.7 + - + +
75B LEU* 4.0 19.6 - - - +
80B GLU* 3.0 32.8 + - - +
311B ARG* 4.1 7.8 - - - +
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Residues in contact with ALA 65 (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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61B GLY 3.1 15.7 + - - +
62B HIS* 3.8 11.4 - - + +
64B ARG* 1.3 79.2 - - - +
66B GLN* 1.3 56.0 + - - +
68B LEU* 3.5 0.9 + - - +
69B GLN* 3.0 54.9 + - - +
75B LEU* 4.6 12.1 - - + +
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Residues in contact with GLN 66 (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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62B HIS* 2.8 39.1 + - + +
63B THR 4.1 2.7 - - - +
65B ALA* 1.3 73.2 - - - +
67B LEU* 1.3 58.3 + - - +
69B GLN* 4.3 7.4 - - - +
70B GLY* 3.1 22.3 + - - -
298B GLY 3.3 26.1 + - - +
299B ILE* 4.0 4.5 - - - +
300B ALA* 3.1 14.7 + - - +
301B ASP* 2.9 44.6 + - - +
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Residues in contact with LEU 67 (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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52B LEU* 3.6 38.8 - - + +
55B LEU* 3.9 16.4 - - + -
56B SER* 3.6 26.5 - - - -
59B THR* 4.3 5.2 - - + +
63B THR 3.2 17.8 + - - +
64B ARG 3.9 2.9 - - - +
65B ALA 3.3 0.2 - - - -
66B GLN* 1.3 76.7 - - - +
68B LEU* 1.3 59.6 + - - +
70B GLY* 3.4 1.9 + - - -
71B LEU* 3.0 36.4 + - + +
299B ILE* 3.8 33.2 - - + -
302B LEU* 4.0 18.6 - - + -
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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 ALA* 5.4 1.8 - - - -
56B SER* 3.5 28.9 - - - +
64B ARG* 3.2 27.3 + - + +
65B ALA 4.2 0.2 - - - +
67B LEU* 1.3 74.2 - - - +
69B GLN* 1.3 62.7 + - - +
71B LEU* 3.4 18.5 + - + -
72B GLY 3.4 0.2 + - - -
73B PHE* 3.1 44.3 + - + +
75B LEU* 3.8 37.0 - - + -
80B GLU* 3.5 27.1 - - + +
83B ILE* 5.1 11.4 - - + -
84B HIS* 5.4 3.4 - - + +
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Residues in contact with GLN 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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65B ALA* 3.0 41.8 + - - +
66B GLN* 4.3 6.0 - - - +
68B LEU* 1.3 74.6 - - - +
70B GLY* 1.3 59.3 + - - +
72B GLY* 3.0 19.8 + - - -
73B PHE 3.9 14.1 - - - +
75B LEU* 4.7 12.7 - - + +
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Residues in contact with GLY 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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24B PHE* 3.5 17.3 - - - -
66B GLN 3.1 19.7 + - - -
67B LEU 3.7 3.4 - - - -
68B LEU 3.3 0.2 - - - -
69B GLN* 1.3 75.8 - - - +
71B LEU* 1.3 58.1 + - - +
72B GLY* 3.3 1.0 + - - -
297B MET* 4.7 15.6 - - - +
298B GLY* 5.2 1.8 - - - -
299B ILE* 4.1 21.8 - - - +
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Residues in contact with LEU 71 (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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20B ALA* 3.4 19.4 - - - +
21B ASN* 4.5 2.3 - - - +
24B PHE* 3.6 34.6 - - + +
49B SER* 4.2 21.7 + - - +
52B LEU* 4.1 23.8 - - + +
53B ALA* 4.0 29.2 - - + +
67B LEU* 3.0 27.5 + - + +
68B LEU* 3.7 11.2 - - + +
69B GLN 3.2 0.6 - - - -
70B GLY* 1.3 76.9 - - - +
72B GLY* 1.3 58.3 + - - +
73B PHE* 3.6 29.6 - - + -
299B ILE* 5.3 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