Contacts of the helix formed by residues 57 - 69 (chain A) in PDB entry 2VSH
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 TRP 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PRO* 4.5 20.3 - - + +
24A PHE* 3.6 38.9 - + + -
53A VAL* 3.4 19.5 - - + +
54A HIS* 2.8 26.9 + + + -
56A ASP* 1.3 86.5 - - + +
58A VAL* 1.3 59.9 + - - +
59A SER 3.4 2.5 - - - -
60A HIS* 3.3 38.0 + + + -
61A ALA* 2.9 30.3 + - - +
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Residues in contact with VAL 58 (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 VAL* 4.0 13.9 - - + +
54A HIS 3.3 12.1 + - - +
55A GLY* 3.6 17.4 + - - +
56A ASP 3.6 2.2 - - - -
57A TRP* 1.3 76.2 - - - +
59A SER* 1.3 64.3 + - - +
61A ALA* 3.2 5.0 + - - +
62A GLU* 3.0 37.3 + - - +
78A ILE* 3.8 25.5 - - + +
79A THR* 4.1 13.5 - - - +
80A LYS* 4.1 10.1 - - + +
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Residues in contact with SER 59 (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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55A GLY 5.2 0.6 + - - -
56A ASP 5.1 4.6 + - - -
57A TRP 3.4 0.2 - - - -
58A VAL* 1.3 78.7 - - - +
60A HIS* 1.3 60.1 + - - +
62A GLU* 3.2 16.3 + - - +
63A ASP* 2.9 36.2 + - - +
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.7 28.8 + + - +
56A ASP 5.5 0.9 - - - +
57A TRP* 3.3 47.0 + + + +
58A VAL 3.2 0.6 - - - -
59A SER* 1.3 80.9 + - - +
61A ALA* 1.3 61.6 + - - +
63A ASP* 3.1 16.2 + - + +
64A LEU* 3.0 47.5 + - + +
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Residues in contact with ALA 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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24A PHE* 4.5 7.4 - - + -
33A LEU* 4.5 6.3 - - + +
53A VAL* 3.9 17.5 - - + -
57A TRP 2.9 13.6 + - - +
58A VAL 3.5 8.1 - - - +
60A HIS* 1.3 76.8 - - - +
62A GLU* 1.3 62.3 + - - +
64A LEU* 3.3 14.6 + - - +
65A VAL* 3.2 26.2 + - - +
78A ILE* 3.9 24.9 - - + -
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Residues in contact with GLU 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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58A VAL* 3.0 27.8 + - - +
59A SER* 3.5 21.6 - - - +
61A ALA* 1.3 72.3 - - - +
63A ASP* 1.3 66.2 + - - +
65A VAL* 3.4 6.1 + - - +
66A ASP* 3.0 31.0 + - - +
73A LYS* 5.4 3.8 - - - +
78A ILE* 3.7 30.8 + - + +
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Residues in contact with ASP 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 SER* 2.9 21.6 + - - +
60A HIS* 3.3 16.9 + - - +
62A GLU* 1.3 76.4 - - - +
64A LEU* 1.3 60.8 + - + +
66A ASP* 3.2 12.5 + - - +
67A LYS* 2.8 31.6 + - - +
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Residues in contact with LEU 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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24A PHE* 3.7 24.0 - - + +
31A PRO* 3.9 31.6 - - + -
33A LEU* 4.7 7.0 - - + -
34A ILE* 4.0 13.0 - - + -
60A HIS* 3.0 48.0 + - + +
61A ALA* 3.5 10.1 - - - +
62A GLU 3.3 0.2 - - - -
63A ASP* 1.3 79.8 - - + +
65A VAL* 1.3 53.1 + - - +
67A LYS* 4.4 4.0 - - + -
68A TYR* 2.7 54.2 + - + +
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Residues in contact with VAL 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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33A LEU* 6.4 0.4 - - + -
34A ILE* 4.5 5.4 - - + -
37A ILE* 4.7 11.4 - - + -
61A ALA 3.2 14.0 + - - +
62A GLU* 3.7 8.7 - - - +
64A LEU* 1.3 73.4 - - - +
66A ASP* 1.3 61.6 + - - +
69A LEU* 2.8 42.4 + - + +
70A PRO* 3.8 0.2 - - - +
73A LYS* 4.0 31.0 - - + -
76A ILE* 4.0 45.5 - - + -
78A ILE* 4.2 11.7 - - + -
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Residues in contact with ASP 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 GLU* 3.0 20.8 + - - +
63A ASP* 3.2 13.5 + - - +
65A VAL* 1.3 76.8 - - - +
67A LYS* 1.3 60.5 + - - +
70A PRO* 3.4 21.5 - - - +
73A LYS* 3.1 41.2 + - - +
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Residues in contact with LYS 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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63A ASP 2.8 17.6 + - - +
64A LEU* 3.7 6.3 - - + +
66A ASP* 1.3 79.5 - - - +
68A TYR* 1.3 99.6 + - + +
70A PRO* 4.0 5.9 - - - +
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Residues in contact with TYR 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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26A GLU* 5.2 2.4 + - - -
29A ASP 3.7 12.9 + - - -
30A ARG* 3.3 35.2 - - + -
31A PRO* 3.6 28.6 - - + +
34A ILE* 3.7 25.2 - - + +
38A GLU* 5.0 1.9 - - - +
64A LEU* 2.7 38.2 + - + +
67A LYS* 1.3 113.0 + - + +
69A LEU* 1.3 65.6 + - - +
70A PRO* 3.4 8.1 - - - +
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Residues in contact with LEU 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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34A ILE* 3.8 29.8 - - + +
37A ILE* 3.7 32.8 - - + -
38A GLU* 3.6 31.4 - - + +
41A VAL* 5.1 2.5 - - + -
65A VAL* 2.8 16.8 + - + +
68A TYR* 1.3 85.9 - - - +
70A PRO* 1.4 59.6 - - - +
71A LEU* 3.1 3.1 - - - -
72A TYR* 2.9 43.2 + - + -
73A LYS 3.4 7.6 + - - -
76A ILE* 4.1 13.9 - - + -
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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