Contacts of the helix formed by residues 51 - 60 (chain B) in PDB entry 5XVO
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 THR 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.2 16.8 - - + -
44A THR 3.0 23.1 + - - +
45A THR* 3.2 8.8 - - - +
47A ILE* 2.7 51.0 + - + +
49A LEU* 4.1 20.4 - - + -
66A PHE* 5.1 4.0 - - + -
67A CYS 5.0 3.4 - - - +
50B THR* 1.3 71.1 - - - +
52B MET* 1.3 59.3 + - - +
54B LEU* 3.3 12.4 + - + +
55B LYS* 2.9 28.9 + - - +
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Residues in contact with MET 52 (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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45A THR* 3.3 45.9 + - - +
69A ASP* 4.6 12.8 - - - +
16B TYR* 3.9 29.2 - - + +
50B THR* 3.2 8.2 + - - +
51B THR* 1.3 73.6 - - - +
53B LEU* 1.3 67.1 + - - +
55B LYS* 3.1 13.2 + - + +
56B ARG* 3.0 50.3 + - + +
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Residues in contact with LEU 53 (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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14B LEU* 3.6 34.5 - - + +
15B SER 3.8 21.8 - - - +
16B TYR* 3.8 24.6 - - + +
21B LEU* 3.9 29.4 - - + -
34B LEU* 4.7 3.4 - - + -
40B LEU* 5.2 0.7 - - + -
49B LEU* 4.6 7.9 - - + -
50B THR* 3.1 20.9 + - - +
52B MET* 1.3 79.8 - - - +
54B LEU* 1.3 58.0 + - + +
56B ARG* 3.1 2.4 + - - -
57B LEU* 2.8 50.7 + - + +
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Residues in contact with LEU 54 (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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49A LEU* 4.8 6.1 - - + -
54A LEU* 5.6 2.5 - - + -
66A PHE* 3.5 40.2 - - + -
49B LEU* 3.6 31.9 - - + -
50B THR 3.2 11.8 + - - +
51B THR* 3.6 14.8 - - + +
52B MET 3.2 0.2 - - - -
53B LEU* 1.3 77.3 - - + +
55B LYS* 1.3 65.1 + - - +
57B LEU* 3.4 18.0 + - + +
58B ILE* 3.0 32.2 + - + +
64B VAL* 4.8 6.7 - - + -
66B PHE* 5.1 3.4 - - + -
77B ILE* 3.6 25.1 - - + -
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Residues in contact with LYS 55 (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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45A THR* 4.5 8.3 - - + -
66A PHE* 6.2 0.6 - - - +
67A CYS 4.1 14.1 - - - +
68A ASP* 4.3 10.6 + - - -
69A ASP* 3.7 33.4 - - - +
74A ILE* 4.0 22.2 - - + +
51B THR 2.9 13.7 + - - +
52B MET* 3.4 20.0 - - + +
54B LEU* 1.3 75.1 - - - +
56B ARG* 1.3 74.9 + - + +
58B ILE* 3.0 6.1 + - - +
59B ASP* 2.5 63.9 + - - +
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Residues in contact with ARG 56 (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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16B TYR* 2.9 42.7 + - + -
19B ASN* 2.5 33.5 + - - +
34B LEU* 3.8 10.1 - - + +
52B MET* 3.0 41.1 + - + +
53B LEU 3.7 3.1 - - - +
55B LYS* 1.3 83.1 - - + +
57B LEU* 1.3 61.8 + - - +
59B ASP* 3.0 43.0 + - - +
60B GLU* 3.2 46.9 + - - +
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Residues in contact with LEU 57 (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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21B LEU* 4.8 2.7 - - + -
34B LEU* 3.9 15.0 - - + -
37B ILE* 5.2 1.8 - - + -
40B LEU* 3.6 30.5 - - + -
53B LEU* 2.8 39.8 + - + +
54B LEU* 3.6 18.2 - - + +
56B ARG* 1.3 78.1 - - - +
58B ILE* 1.3 60.9 + - + +
60B GLU 3.6 0.9 + - - -
61B LYS 3.3 3.1 + - - -
62B ILE* 3.2 67.8 + - + +
64B VAL* 3.9 20.9 - - + -
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Residues in contact with ILE 58 (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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66A PHE* 4.3 18.6 - - + -
74A ILE* 4.0 39.5 - - + +
75A GLY* 4.6 4.3 - - - -
54B LEU 3.0 21.3 + - - +
55B LYS 3.0 6.5 + - - +
57B LEU* 1.3 74.9 - - - +
59B ASP* 1.3 67.4 + - - +
61B LYS* 3.0 28.5 + - - +
62B ILE 5.5 1.3 - - - -
64B VAL* 6.1 0.4 - - + -
77B ILE* 3.8 36.1 - - + -
79B PRO* 3.9 25.5 - - + +
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Residues in contact with ASP 59 (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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74A ILE* 5.2 5.7 - - - +
55B LYS* 2.5 51.9 + - - +
56B ARG* 3.0 33.5 + - - +
58B ILE* 1.3 79.8 - - - +
60B GLU* 1.3 65.1 + - - +
61B LYS* 3.2 15.2 + - - +
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Residues in contact with GLU 60 (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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1B MET* 3.6 23.0 + - + +
19B ASN* 5.0 3.3 + - - +
34B LEU* 4.1 24.0 - - + +
35B SER* 4.4 19.8 + - - -
56B ARG* 3.2 41.1 + - - +
57B LEU 4.0 0.2 - - - +
58B ILE 3.4 0.2 - - - -
59B ASP* 1.3 82.2 - - - +
61B LYS* 1.3 65.1 + - - +
62B ILE* 3.4 20.8 + - + -
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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