Contacts of the helix formed by residues 50 - 62 (chain C) in PDB entry 4XYN
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 GLU 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ILE* 3.8 0.7 - - - +
49C LYS* 1.3 87.7 - - + +
51C GLN* 1.3 66.5 + - - +
52C GLU* 3.8 16.7 - - + +
53C VAL* 3.3 28.2 + - + +
54C VAL* 3.4 15.3 + - - +
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Residues in contact with GLN 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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30C LYS* 4.5 2.8 - - - +
49C LYS 3.8 2.4 + - - -
50C GLU* 1.3 71.3 + - - +
52C GLU* 1.3 73.8 + - - +
54C VAL* 3.0 21.3 + - - +
55C ASP* 2.7 59.3 + - - +
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Residues in contact with GLU 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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63A ASN 4.8 2.2 - - - +
64A ASP* 2.7 54.9 - - + +
50C GLU* 3.3 15.4 - - + +
51C GLN* 1.3 88.7 + - + +
53C VAL* 1.3 61.3 + - + +
55C ASP* 3.9 10.9 - - - +
56C LYS* 3.1 35.7 + - + +
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Residues in contact with VAL 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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48C ILE* 3.8 30.3 - - + -
49C LYS 5.8 0.7 - - - +
50C GLU* 3.3 25.9 + - + +
51C GLN 3.1 0.6 - - - -
52C GLU* 1.3 76.9 - - + +
54C VAL* 1.3 65.6 + - - +
56C LYS* 3.3 6.1 + - - +
57C VAL* 3.0 33.6 + - + +
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Residues in contact with VAL 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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30C LYS* 3.5 43.1 - - + +
33C LEU* 5.4 3.2 - - + +
34C LYS* 4.0 22.0 - - + +
48C ILE* 3.4 27.4 - - + -
50C GLU 3.4 8.7 + - - +
51C GLN* 3.2 23.1 - - - +
53C VAL* 1.3 76.0 - - - +
55C ASP* 1.3 64.2 + - - +
57C VAL* 3.1 8.7 + - - +
58C MET* 2.9 21.7 + - + +
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Residues in contact with ASP 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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30C LYS* 2.7 40.7 + - - +
51C GLN* 2.7 53.4 + - - +
52C GLU* 3.9 10.9 - - - +
53C VAL 3.3 0.2 - - - -
54C VAL* 1.3 72.9 - - - +
56C LYS* 1.3 57.4 + - + +
58C MET* 3.4 2.3 + - - +
59C GLU* 2.8 40.5 + - + +
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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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63A ASN* 6.0 3.5 - - - +
52C GLU* 3.1 26.7 + - + +
53C VAL* 3.8 6.3 - - - +
55C ASP* 1.3 74.2 - - + +
57C VAL* 1.3 63.8 + - + +
59C GLU* 3.3 33.5 + - - +
60C THR* 3.0 25.6 + - - -
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Residues in contact with VAL 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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33C LEU* 4.0 20.4 - - + -
37C ILE* 4.5 12.8 - - + -
48C ILE* 4.5 15.7 - - + -
53C VAL* 3.0 23.9 + - + +
54C VAL* 3.5 6.7 - - - +
56C LYS* 1.3 73.2 - - + +
58C MET* 1.3 67.1 + - - +
60C THR* 3.0 10.1 + - - -
61C LEU* 2.9 33.5 + - + +
77C PHE* 4.5 9.4 - - + -
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Residues in contact with MET 58 (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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28C LEU 3.5 18.4 - - - +
29C LYS 3.7 0.7 - - - -
30C LYS* 3.3 54.7 - - + +
33C LEU* 4.0 21.1 - - + -
54C VAL 2.9 14.2 + - - +
55C ASP 3.7 4.0 - - - +
57C VAL* 1.3 80.1 - - - +
59C GLU* 1.3 55.9 + - - +
61C LEU* 4.4 1.8 - - - +
62C ASP* 2.8 46.5 + - + +
67C GLY* 3.7 21.1 - - - +
68C GLU* 4.0 17.7 - - - +
69C CYS* 4.1 7.4 - - + +
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Residues in contact with GLU 59 (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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55C ASP* 2.8 29.1 + - + +
56C LYS* 3.4 44.2 + - + +
57C VAL 3.2 0.2 - - - -
58C MET* 1.3 75.4 - - - +
60C THR* 1.3 62.6 + - - +
62C ASP* 3.6 13.3 - - - +
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Residues in contact with THR 60 (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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56C LYS 3.0 12.8 + - - -
57C VAL* 3.0 11.1 + - - -
59C GLU* 1.3 80.4 - - - +
61C LEU* 1.3 61.9 + - + +
63C ASN* 3.0 20.8 + - - +
80C MET* 4.3 27.0 - - + +
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Residues in contact with LEU 61 (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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33C LEU* 4.0 25.4 - - + -
57C VAL* 2.9 21.9 + - + +
58C MET* 4.2 3.6 - - - +
60C THR* 1.3 78.0 - - + +
62C ASP* 1.3 61.8 + - - +
63C ASN* 2.9 17.7 + - - +
69C CYS* 4.0 19.5 - - + -
73C GLU* 3.2 27.9 - - - +
76C ALA* 5.5 1.1 - - + -
77C PHE* 3.5 61.5 - - + +
80C MET* 3.9 20.9 - - + -
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Residues in contact with ASP 62 (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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58C MET* 2.8 27.2 + - + +
59C GLU* 3.6 15.0 - - - +
61C LEU* 1.3 73.3 - - - +
63C ASN* 1.3 59.6 + - - +
64C ASP* 3.3 1.0 - - - +
65C GLY* 2.8 39.5 + - - -
67C GLY* 3.0 23.0 + - - -
68C GLU 4.1 8.1 - - - +
73C GLU* 3.3 6.2 - - - +
502C CA 2.8 24.1 - - - -
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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