Contacts of the helix formed by residues 59 - 71 (chain C) in PDB entry 3UDB
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 ASP 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C GLU 3.3 10.0 + - - +
57C LYS* 4.2 13.9 - - - +
58C ILE* 1.3 82.5 - - - +
60C GLU* 1.3 54.5 + - - +
61C ASN* 3.1 24.2 + - - +
62C VAL* 2.7 28.1 + - - +
63C LYS 3.6 0.3 + - - -
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C ASP* 1.3 74.1 - - - +
61C ASN* 1.3 55.7 + - - +
63C LYS* 2.3 67.2 + - - +
64C ARG* 2.5 34.3 + - + +
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Residues in contact with ASN 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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59C ASP* 2.9 14.0 + - - +
60C GLU* 1.3 83.5 - - - +
62C VAL* 1.3 61.6 + - + +
64C ARG* 2.2 44.5 + - - +
65C GLU* 3.3 32.9 + - - +
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Residues in contact with VAL 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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52C ILE* 3.4 35.9 - - + -
57C LYS 4.6 10.1 - - - +
58C ILE* 4.7 13.2 - - + +
59C ASP* 2.7 20.9 + - - +
61C ASN* 1.3 75.2 - - + +
63C LYS* 1.3 62.3 + - - +
65C GLU* 3.7 11.7 + - - +
66C ILE* 3.1 42.2 + - + +
90C LEU* 4.6 7.9 - - + -
312C ILE* 5.8 0.9 - - + -
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Residues in contact with LYS 63 (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 ILE 5.3 1.6 - - - +
59C ASP 3.6 2.3 + - - +
60C GLU* 2.3 69.9 + - - +
62C VAL* 1.3 71.5 - - - +
64C ARG* 1.3 62.3 + - - +
66C ILE* 3.5 1.6 + - - +
67C ILE* 3.2 28.6 + - + +
309C MET* 3.5 37.4 - - + +
312C ILE* 4.4 27.3 - - + +
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Residues in contact with ARG 64 (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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60C GLU* 2.5 34.4 + - + +
61C ASN* 2.2 35.3 + - - +
63C LYS* 1.3 73.1 - - - +
65C GLU* 1.3 88.2 + - - +
67C ILE* 3.3 5.7 + - - +
68C ASN* 2.9 59.4 + - - +
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Residues in contact with GLU 65 (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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61C ASN* 3.3 22.0 + - - +
62C VAL* 4.0 13.8 - - - +
64C ARG* 1.3 98.6 + - - +
66C ILE* 1.3 57.0 + - - +
68C ASN* 3.7 7.1 - - - +
69C HIS* 2.9 32.6 + - - +
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Residues in contact with ILE 66 (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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62C VAL* 3.1 23.0 + - + +
63C LYS 3.8 4.7 - - - +
64C ARG 3.3 0.4 - - - -
65C GLU* 1.3 77.5 - - + +
67C ILE* 1.3 58.7 + - + +
69C HIS* 3.9 5.1 - - - +
70C ARG* 2.9 27.1 + - + +
80C PHE* 4.1 22.1 - - + -
83C VAL* 3.9 11.9 - - + -
90C LEU* 3.9 23.8 - - + -
92C ILE* 4.1 23.3 - - + -
308C ILE* 4.1 23.3 - - + -
312C ILE* 3.8 21.1 - - + -
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Residues in contact with ILE 67 (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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63C LYS* 3.2 21.0 + - + +
64C ARG* 3.8 4.9 - - - +
66C ILE* 1.3 74.3 - - + +
68C ASN* 1.3 72.5 + - - +
70C ARG* 3.1 17.6 + - + +
71C SER* 3.1 14.5 + - - -
305C ILE* 4.2 34.3 - - + -
308C ILE* 4.4 18.8 - - + -
309C MET* 4.2 26.0 - - - -
312C ILE* 5.5 0.7 - - + -
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Residues in contact with ASN 68 (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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64C ARG* 2.9 47.2 + - - +
65C GLU* 3.7 6.7 - - - +
67C ILE* 1.3 82.3 - - - +
69C HIS* 1.3 60.4 + - - +
71C SER* 2.7 24.8 + - - -
72C LEU* 3.7 10.5 - - - +
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Residues in contact with HIS 69 (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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65C GLU 2.9 18.3 + - - +
66C ILE* 4.0 4.5 - - - +
68C ASN* 1.3 75.5 - - - +
70C ARG* 1.3 62.2 + - - +
71C SER 3.2 0.9 + - - -
72C LEU* 3.2 32.2 + - + +
77C ILE* 5.4 0.4 - - + -
78C VAL* 2.3 34.0 + - + +
79C ARG* 3.9 4.9 - - - -
80C PHE* 3.5 32.6 + - + +
92C ILE* 5.8 2.0 - - - +
94C MET* 4.1 28.1 - - + +
160C ASP* 5.2 17.7 + - + +
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Residues in contact with ARG 70 (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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66C ILE* 2.9 20.3 + - + +
67C ILE* 3.1 13.6 + - + +
69C HIS* 1.3 78.9 - - - +
71C SER* 1.3 59.1 + - - +
72C LEU 3.5 1.2 + - - +
73C ARG* 3.3 52.8 + - - +
80C PHE* 3.4 37.5 + - + +
302C GLY 4.5 2.8 + - - -
303C GLN 2.3 37.0 + - - -
304C SER* 3.5 7.9 - - - +
305C ILE* 3.5 36.5 - - - +
308C ILE* 3.6 15.6 - - + +
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Residues in contact with SER 71 (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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67C ILE* 3.1 10.8 + - - -
68C ASN* 2.7 21.5 + - - -
69C HIS 3.1 0.2 - - - -
70C ARG* 1.3 77.3 - - - +
72C LEU* 1.3 67.0 + - - +
73C ARG* 3.3 18.1 + - - +
130C TYR* 3.7 7.8 + - - -
134C MET* 4.0 18.7 - - - +
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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