Contacts of the helix formed by residues 60 - 68 (chain A) in PDB entry 2UVV
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 PRO 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLY 3.6 10.8 - - - +
42A ALA* 4.4 1.3 - - + -
58A GLY 4.2 2.9 - - - +
59A ILE* 1.3 93.7 - - + +
61A ILE* 1.3 66.6 + - - +
62A VAL* 3.7 21.8 - - + -
63A GLU* 3.0 30.2 + - + +
64A ALA 3.1 8.8 + - - -
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Residues in contact with ILE 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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31A CYS* 3.4 38.4 - - + -
32A VAL 3.9 6.1 - - - +
33A PHE* 3.6 26.2 - - + -
39A ASP* 3.3 17.0 - - + +
40A SER 3.9 4.9 - - - +
41A GLY 3.1 27.4 + - - +
42A ALA 3.7 13.5 - - - +
43A VAL* 4.2 3.1 - - + +
59A ILE 3.6 0.8 + - - -
60A PRO* 1.3 71.0 - - - +
62A VAL* 1.3 63.9 + - - +
64A ALA* 3.0 9.4 + - - +
65A LYS* 3.0 45.6 + - + +
73A TYR* 4.6 2.2 - - + -
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Residues in contact with VAL 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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37A PHE* 4.1 22.9 - - + -
38A GLU 4.3 1.1 - - - +
39A ASP* 3.6 30.0 + - + +
40A SER* 5.2 0.2 - - - -
60A PRO* 3.7 18.8 - - + -
61A ILE* 1.3 78.1 - - - +
63A GLU* 1.3 73.2 + - + +
65A LYS* 3.6 6.8 + - - +
66A LYS* 3.3 37.2 + - - +
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Residues in contact with GLU 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 ILE* 4.6 8.5 - - + -
60A PRO* 3.0 36.9 + - + +
62A VAL* 1.3 78.5 - - + +
64A ALA* 1.3 64.7 + - - +
66A LYS* 3.0 49.2 + - - +
67A ILE* 3.2 21.3 + - + +
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Residues in contact with ALA 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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43A VAL* 4.0 9.2 - - + -
55A VAL* 3.9 29.6 - - + +
59A ILE* 3.9 12.7 - - + +
60A PRO 3.1 9.3 + - - +
61A ILE 3.0 9.6 + - - +
63A GLU* 1.3 78.1 - - - +
65A LYS* 1.3 56.7 + - - +
67A ILE* 3.2 4.2 + - - +
68A LEU* 2.8 27.5 + - - +
73A TYR* 3.1 22.9 + - + +
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Residues in contact with LYS 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 PHE* 4.9 4.6 - - - -
39A ASP* 2.7 44.0 + - + +
61A ILE* 3.0 22.8 + - + +
62A VAL* 4.1 6.3 - - - +
63A GLU 3.3 0.2 - - - -
64A ALA* 1.3 73.4 - - - +
66A LYS* 1.3 61.7 + - - +
69A PRO* 3.0 38.1 - - + +
73A TYR* 3.4 53.8 - - + +
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Residues in contact with LYS 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 VAL* 3.3 23.5 + - - +
63A GLU* 3.0 46.4 + - - +
65A LYS* 1.3 79.0 - - - +
67A ILE* 1.3 64.5 + - + +
69A PRO* 3.6 7.4 - - - +
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Residues in contact with ILE 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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53A PHE* 3.2 43.1 - - + +
54A GLY* 4.5 10.5 - - - +
55A VAL* 4.3 12.6 - - + -
59A ILE* 5.0 4.0 - - + -
63A GLU* 3.4 18.6 - - + +
64A ALA* 3.2 5.5 + - - +
66A LYS* 1.3 82.2 - - + +
68A LEU* 1.3 66.8 + - + +
69A PRO* 3.4 6.5 - - - +
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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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27A PRO* 4.1 16.2 - - + -
29A VAL* 5.3 0.4 - - + -
50A ALA* 3.8 32.3 - - + +
53A PHE* 3.7 32.1 - - + -
55A VAL* 3.6 25.4 - - + -
64A ALA 2.8 12.3 + - - +
65A LYS 3.6 1.8 - - - -
67A ILE* 1.3 85.2 - - + +
69A PRO* 1.3 67.3 - - - +
70A ASN 2.9 4.6 + - - -
71A ALA* 3.0 18.8 + - + +
73A TYR* 2.9 17.1 + - - +
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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