Contacts of the helix formed by residues 58 - 70 (chain C) in PDB entry 1UU1
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 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C TYR* 3.1 26.4 + - - -
55C ASP* 3.7 12.5 - - - +
56C SER 2.4 15.9 + - - +
57C PRO* 1.3 68.1 - - - +
59C GLU* 1.3 72.8 + - - +
60C GLU* 4.1 13.1 + - - +
61C LEU* 3.1 8.8 + - + +
62C ILE* 3.0 24.7 + - - +
238C GLN* 2.6 24.1 - - - +
242C LYS* 2.8 35.9 + - - +
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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* 5.6 1.2 + - - +
57C PRO 3.7 3.2 + - - -
58C ASP* 1.3 76.0 + - - +
60C GLU* 1.3 66.6 + - + +
62C ILE* 3.1 9.4 + - - +
63C GLU* 3.1 41.7 + - + +
76C LYS* 5.1 13.6 - - + +
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Residues in contact with GLU 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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44C ARG* 4.8 5.0 + - - -
54C TYR* 4.6 5.5 + - - -
58C ASP* 3.3 7.6 - - - +
59C GLU* 1.3 79.5 - - + +
61C LEU* 1.3 62.1 + - - +
63C GLU* 3.1 17.9 + - - +
64C LYS* 3.2 33.2 + - - +
239C MET* 4.8 3.1 - - - +
242C LYS* 2.9 36.0 + - + +
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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
----------------------------------------------------------
56C SER 4.9 2.0 - - - +
57C PRO* 5.8 0.2 - - + -
58C ASP* 3.1 21.8 + - + +
60C GLU* 1.3 77.1 - - - +
62C ILE* 1.3 64.4 + - + +
64C LYS* 3.3 2.4 + - + +
65C ILE* 2.9 51.9 + - + +
81C VAL* 4.5 23.1 - - + -
200C PHE* 4.9 0.4 - - + -
211C VAL* 4.9 5.6 - - + -
238C GLN* 3.9 30.5 - - + +
241C ALA* 4.3 17.5 - - + -
242C LYS* 3.9 25.0 - - + +
245C LEU* 4.5 9.9 - - + -
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PRO* 4.4 22.0 - - + +
58C ASP 3.0 19.9 + - - +
59C GLU* 3.1 9.4 + - - +
61C LEU* 1.3 80.0 - - + +
63C GLU* 1.3 53.5 + - + +
65C ILE* 3.2 7.8 + - + +
66C LEU* 2.8 53.7 + - + +
76C LYS* 3.5 31.0 - - + +
79C VAL* 4.0 33.0 - - + +
80C SER* 4.6 5.6 - - - -
81C VAL* 5.5 2.2 - - + -
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Residues in contact with GLU 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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59C GLU* 3.2 27.0 - - + +
60C GLU* 3.1 28.8 + - - +
61C LEU 3.2 0.2 - - - -
62C ILE* 1.3 78.5 - - + +
64C LYS* 1.3 54.2 + - + +
66C LEU* 3.2 9.4 + - - +
67C SER* 2.7 36.2 + - - -
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Residues in contact with LYS 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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44C ARG* 4.7 4.4 - - - +
60C GLU* 3.2 19.0 + - - +
61C LEU* 3.6 3.8 - - - +
63C GLU* 1.3 73.8 - - + +
65C ILE* 1.3 56.2 + - - +
67C SER* 3.3 8.7 + - - -
68C TYR* 2.7 34.3 + - - +
242C LYS* 3.6 42.0 - - + +
245C LEU* 3.6 20.7 - - + +
246C ASP* 3.0 38.0 + - - -
248C ARG* 3.8 4.2 + - - +
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Residues in contact with ILE 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 LEU* 2.9 39.6 + - + +
62C ILE* 3.2 11.6 + - + +
64C LYS* 1.3 74.1 - - - +
66C LEU* 1.3 55.1 + - - +
68C TYR* 2.8 9.0 + - + +
69C LEU* 2.6 59.4 + - + +
79C VAL* 3.8 19.1 - - + -
200C PHE* 3.8 27.1 - - + -
213C TYR* 3.7 41.3 - - + -
245C LEU* 4.0 2.7 - - + +
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Residues in contact with LEU 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 ILE* 2.8 45.4 + - + +
63C GLU* 3.4 10.3 - - - +
65C ILE* 1.3 72.0 - - - +
67C SER* 1.3 62.2 + - - +
69C LEU* 3.0 18.3 + - + +
70C ASP* 3.0 10.2 + - - -
71C THR* 4.1 11.8 + - + +
74C LEU* 3.2 49.6 - - + +
75C SER* 3.9 11.4 - - - +
76C LYS* 3.9 3.6 - - + +
79C VAL* 3.6 22.7 - - + -
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Residues in contact with SER 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 GLU 2.7 20.6 + - - -
64C LYS* 3.4 9.9 - - - -
66C LEU* 1.3 71.8 - - - +
68C TYR* 1.3 62.7 + - - +
70C ASP* 3.1 18.1 + - - +
248C ARG* 3.8 20.2 + - - -
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Residues in contact with TYR 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 LYS 2.7 19.0 + - - +
65C ILE* 3.2 12.6 - - + +
67C SER* 1.3 74.3 + - - +
69C LEU* 1.3 63.6 + - + +
70C ASP* 3.3 4.3 + - - +
177C TYR* 3.9 11.8 + + - -
178C GLU* 2.8 35.9 + - - +
198C ARG* 4.0 9.6 - - - -
200C PHE* 5.9 0.7 - + - -
204C PHE* 4.1 22.1 - + - -
213C TYR* 3.4 30.7 - + - -
245C LEU* 3.7 24.9 - - + -
248C ARG* 3.7 28.4 + - + +
252C GLU* 5.8 2.9 - - + -
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 2.6 58.0 + - + +
66C LEU* 3.0 11.2 + - - +
68C TYR* 1.3 79.2 - - + +
70C ASP* 1.3 69.3 + - - +
71C THR* 3.0 15.4 + - + +
74C LEU* 4.6 9.4 - - + -
79C VAL* 5.5 2.0 - - + -
185C VAL* 4.1 20.6 - - + -
198C ARG* 4.0 31.4 - - - +
213C TYR* 4.2 7.9 - - + -
215C VAL* 4.3 16.2 - - + -
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Residues in contact with ASP 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 LEU 3.0 7.6 + - - -
67C SER* 3.1 15.2 + - - +
68C TYR 4.1 4.0 - - - +
69C LEU* 1.3 80.5 - - - +
71C THR* 1.3 67.1 + - - +
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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