Contacts of the helix formed by residues 46 - 57 (chain C) in PDB entry 3OX4
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 GLY 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ASN 3.1 10.6 + - - -
44C LYS 2.9 7.4 + - - -
45C SER* 1.3 79.1 + - - +
47C VAL* 1.3 60.3 + - - +
48C VAL 3.3 2.5 - - - -
49C LYS* 3.6 11.1 + - - +
50C GLN* 3.0 28.2 + - - +
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 5.9 0.4 - - + -
42C MET* 3.1 24.1 + - + +
45C SER* 3.1 23.6 - - - +
46C GLY* 1.3 76.6 - - - +
48C VAL* 1.3 66.1 + - - +
50C GLN* 3.1 17.0 - - + +
51C VAL* 3.0 23.6 + - + +
95C LEU* 3.7 31.0 - - + -
179C LEU* 4.2 26.2 - - + +
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 4.0 11.1 - - + +
38C SER* 4.2 10.1 - - - +
42C MET* 3.3 22.2 - - + +
43C ASN* 3.4 29.2 - - + +
47C VAL* 1.3 76.8 - - - +
49C LYS* 1.3 59.3 + - - +
51C VAL* 3.0 6.1 + - - +
52C ALA* 2.7 25.7 + - + +
64C VAL* 3.7 36.8 - - + -
95C LEU* 3.7 20.0 - - + -
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASN 5.5 0.2 + - - -
46C GLY* 3.6 13.0 + - - +
47C VAL 3.3 0.2 - - - -
48C VAL* 1.3 77.0 - - - +
50C GLN* 1.3 55.1 + - - +
52C ALA* 3.7 18.4 - - + +
53C ASP* 2.7 73.4 + - - +
56C LYS* 4.6 13.1 - - - +
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Residues in contact with GLN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.1 21.1 - - + +
20C GLU* 5.8 3.0 + - - +
46C GLY 3.0 14.4 + - - +
47C VAL* 3.1 24.0 + - - +
49C LYS* 1.3 75.5 - - - +
51C VAL* 1.3 58.9 + - + +
53C ASP* 3.9 6.4 - - - +
54C LEU* 3.1 39.0 + - + +
179C LEU* 4.1 16.6 - - - +
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.5 23.3 - - + -
23C ILE* 4.3 14.8 - - + -
36C ILE* 3.9 20.2 - - + -
47C VAL* 3.0 17.9 + - + +
48C VAL* 3.0 7.4 + - - +
50C GLN* 1.3 76.8 - - - +
52C ALA* 1.3 66.4 + - - +
54C LEU* 3.1 4.1 + - - +
55C LEU* 2.9 35.4 + - + +
93C ILE* 4.6 14.1 - - + -
95C LEU* 3.9 26.9 - - + -
136C ILE* 5.4 2.2 - - + -
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.2 6.9 - - + +
48C VAL* 2.7 17.9 + - + +
49C LYS* 3.1 30.5 + - + +
51C VAL* 1.3 75.0 - - - +
53C ASP* 1.3 59.7 + - - +
55C LEU* 3.2 2.7 + - - +
56C LYS* 2.7 41.7 + - - +
62C SER* 3.7 18.4 - - - +
64C VAL* 5.8 1.8 - - + -
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Residues in contact with ASP 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS* 2.7 61.4 + - - +
50C GLN* 3.9 7.0 + - - +
52C ALA* 1.3 73.6 - - - +
54C LEU* 1.3 63.5 + - + +
56C LYS* 3.2 11.1 + - - +
57C ALA* 3.2 20.8 + - - +
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.3 15.9 - - + -
20C GLU* 4.1 33.7 - - + +
23C ILE* 3.6 34.4 - - + +
24C LYS* 5.4 6.5 - - - +
50C GLN* 3.1 23.7 + - + +
51C VAL 3.1 3.2 + - - +
53C ASP* 1.3 79.3 - - + +
55C LEU* 1.3 62.0 + - - +
57C ALA* 3.3 16.4 + - + +
58C GLN* 3.5 18.9 + - - +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 3.6 25.4 - - + -
26C LEU* 3.8 22.7 - - + -
34C ALA* 4.1 15.0 - - + -
36C ILE* 4.2 3.4 - - + -
51C VAL* 2.9 28.0 + - + +
52C ALA* 3.5 6.5 - - - +
54C LEU* 1.3 74.0 - - - +
56C LYS* 1.3 64.7 - - - +
58C GLN* 3.0 10.9 + - - +
59C GLY 3.2 0.2 + - - -
60C ILE* 2.9 46.0 + - + +
62C SER* 4.1 15.5 - - - -
91C PHE* 4.5 0.2 - - + -
93C ILE* 3.6 27.8 - - + -
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS* 4.6 9.4 - - - +
52C ALA* 2.7 44.4 + - - +
53C ASP* 3.3 13.2 - - - +
55C LEU* 1.3 78.3 - - - +
57C ALA* 1.3 55.7 + - - +
58C GLN 2.9 0.2 - - - -
59C GLY* 2.7 23.9 + - - -
60C ILE 3.4 23.8 + - - +
61C ASN* 4.3 6.3 - - - +
62C SER* 2.7 39.7 + - - +
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASN* 4.8 2.1 + - - -
53C ASP 3.2 8.6 + - - +
54C LEU* 3.5 15.5 - - + +
55C LEU 3.2 0.2 - - - -
56C LYS* 1.3 78.5 - - - +
58C GLN* 1.3 70.9 + - - +
59C GLY 3.4 0.6 + - - -
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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