Contacts of the helix formed by residues 60 - 71 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A THR* 1.3 77.1 - - - +
61A GLY* 1.3 67.3 + - - +
63A THR 3.5 0.5 + - - -
64A ARG* 3.3 40.3 + - - +
308A ASN* 3.2 31.5 + - - +
310A SER* 3.6 20.1 + - - +
311A ARG* 3.9 20.9 - - - -
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Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A CYS* 1.3 78.5 - - - +
62A HIS* 1.3 62.5 + - - -
64A ARG* 3.3 7.0 + - - +
65A ALA* 3.3 21.9 + - - +
308A ASN* 4.1 8.7 - - - -
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A CYS 3.6 0.2 + - - -
61A GLY* 1.3 70.4 - - - -
63A THR* 1.3 65.0 + - - +
65A ALA* 4.1 5.9 - - + +
66A GLN* 3.1 42.7 + - + +
301A ASP* 2.7 28.1 + - - +
308A ASN* 5.0 2.0 - - - +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 4.3 3.6 - - + -
60A CYS 3.5 7.6 + - - -
61A GLY 3.3 0.6 - - - -
62A HIS* 1.3 78.9 - - - +
64A ARG* 1.3 60.9 + - - +
66A GLN* 3.9 1.8 - - - +
67A LEU* 3.1 24.6 + - - +
301A ASP* 3.7 28.2 + - + +
302A LEU* 3.6 31.4 - - + +
306A GLN 4.3 2.4 + - - -
307A ALA* 3.9 1.7 - - - -
308A ASN* 3.0 39.3 + - - +
309A PHE* 4.2 6.3 - - + -
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A SER* 4.0 6.3 - - - +
59A THR* 3.4 35.6 + - - +
60A CYS* 3.3 40.8 + - - +
61A GLY 3.3 11.2 + - - +
63A THR* 1.3 78.5 - - - +
65A ALA* 1.3 62.9 + - - +
67A LEU* 3.2 4.1 + - - +
68A LEU* 3.0 51.1 + - + +
75A LEU* 5.2 8.8 - - - +
80A GLU* 4.3 11.3 + - - +
311A ARG* 3.5 19.5 - - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY 3.3 13.5 + - - +
62A HIS* 4.1 7.4 - - + +
64A ARG* 1.3 80.7 - - - +
66A GLN* 1.3 56.6 + - - +
68A LEU* 4.2 1.1 - - - +
69A GLN* 3.1 37.6 + - - +
75A LEU* 4.4 29.9 - - + +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 3.1 37.3 + - + +
63A THR 3.9 3.8 - - - +
65A ALA* 1.3 74.4 - - - +
67A LEU* 1.3 59.8 + - - +
69A GLN* 4.2 3.8 - - - +
70A GLY* 3.1 23.6 + - - -
298A GLY 3.1 25.9 + - - +
299A ILE* 3.9 9.6 - - - +
300A ALA* 3.0 12.3 + - - +
301A ASP* 2.9 49.3 + - - +
302A LEU 4.8 0.3 + - - -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.7 41.7 - - + +
55A LEU* 3.9 15.3 - - + -
56A SER* 3.8 23.8 - - - +
59A THR* 4.3 7.2 - - + +
63A THR 3.1 16.6 + - - +
64A ARG 3.6 3.8 - - - +
66A GLN* 1.3 74.5 - - - +
68A LEU* 1.3 58.9 + - - +
70A GLY* 3.2 2.6 + - - -
71A LEU* 2.9 46.8 + - + +
299A ILE* 3.9 31.2 - - + +
302A LEU* 4.1 12.8 - - + -
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA* 5.7 0.4 - - - -
56A SER* 3.6 29.2 - - - +
64A ARG* 3.0 40.6 + - + +
65A ALA 4.2 2.2 - - - +
67A LEU* 1.3 76.2 - - - +
69A GLN* 1.3 57.8 + - - +
71A LEU* 3.3 9.4 + - + +
72A GLY 3.1 7.8 + - - -
73A PHE* 2.9 43.8 + - + +
75A LEU* 3.8 30.5 - - + -
80A GLU* 4.5 14.8 - - + -
83A ILE* 4.0 26.5 - - + -
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 3.1 22.7 + - - +
66A GLN* 4.2 4.2 - - - +
68A LEU* 1.3 74.2 - - - +
70A GLY* 1.3 64.8 + - - +
72A GLY* 3.2 13.9 + - - -
73A PHE 3.9 12.5 + - - +
75A LEU* 5.3 10.1 - - + +
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.4 15.4 - - - +
66A GLN 3.1 16.5 + - - -
67A LEU 3.2 3.8 + - - -
69A GLN* 1.3 78.2 - - - +
71A LEU* 1.3 57.9 + - - +
72A GLY* 3.1 1.3 + - - -
297A MET* 4.3 19.4 - - - +
298A GLY 5.8 0.2 - - - -
299A ILE* 3.9 19.7 - - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA 3.7 16.6 - - - +
21A ASN* 5.0 1.0 - - - +
24A PHE* 3.7 42.2 - - + +
49A SER* 4.3 14.9 + - - +
52A LEU* 3.8 46.9 - - + +
53A ALA* 4.0 7.0 - - + +
67A LEU* 2.9 32.0 + - + +
68A LEU* 3.7 8.7 - - + +
69A GLN 3.3 0.2 - - - -
70A GLY* 1.3 75.5 - - - +
72A GLY* 1.3 57.9 + - - +
73A PHE* 3.6 32.9 - - + -
299A ILE* 5.0 1.1 - - + -
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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