Contacts of the helix formed by residues 67 - 75 (chain R) in PDB entry 2UZI
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 MET 67 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57H THR* 5.8 0.4 - - - -
59H TYR* 4.2 10.3 - - - +
36R ILE* 3.7 31.4 - - + +
37R GLU* 3.9 27.1 - - - +
59R ALA* 6.0 0.2 - - - -
64R TYR* 3.0 49.5 + - + +
66R ALA* 1.3 76.8 - - - +
68R ARG* 1.3 63.3 + - - +
69R ASP 3.3 1.3 + - - -
70R GLN* 3.3 32.5 + - - +
71R TYR* 3.4 19.1 + - + -
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Residues in contact with ARG 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59R ALA 4.8 6.8 + - - -
60R GLY 4.6 6.1 + - - -
61R GLN 4.6 2.6 + - - -
62R GLU* 4.6 15.2 - - - +
64R TYR 5.0 0.2 - - - +
65R SER* 2.9 47.6 + - - +
67R MET* 1.3 78.6 - - - +
69R ASP* 1.3 60.5 + - - +
71R TYR* 2.8 32.3 + - + +
72R MET* 3.0 50.2 + - + +
96R TYR* 3.7 30.7 + - - -
99R GLN* 2.8 43.5 + - - +
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Residues in contact with ASP 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R SER 4.5 0.2 + - - -
66R ALA 3.8 6.9 + - - +
67R MET 3.3 1.2 - - - -
68R ARG* 1.3 79.5 - - - +
70R GLN* 1.3 68.8 + - + +
73R ARG* 3.4 22.0 + - - +
102R ARG* 5.7 2.6 + - - -
103R VAL* 3.7 27.6 - - - +
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Residues in contact with GLN 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66R ALA 2.8 23.1 + - - +
67R MET* 3.4 30.0 + - - +
69R ASP* 1.3 81.2 + - - +
71R TYR* 1.3 64.5 + - - +
73R ARG* 3.2 26.1 + - - +
74R THR* 3.2 19.1 + - + +
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Residues in contact with TYR 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R VAL* 3.6 20.8 - - + +
9R VAL* 4.1 11.8 - - + +
37R GLU* 3.4 20.9 - - - +
56R LEU* 3.1 26.5 - - + -
58R THR* 3.6 33.8 + - + -
59R ALA 4.7 5.3 + - - -
64R TYR 5.6 0.4 + - - -
67R MET* 3.4 22.5 + - + -
68R ARG* 2.8 42.7 + - + +
70R GLN* 1.3 76.9 - - - +
72R MET* 1.3 85.6 + - + +
74R THR* 3.8 8.0 + - - +
75R GLY* 2.9 27.4 + - - -
96R TYR* 6.0 0.9 - - - -
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Residues in contact with MET 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9R VAL* 5.0 3.4 - - + -
68R ARG* 3.0 39.9 + - + +
69R ASP* 5.7 0.2 - - - +
71R TYR* 1.3 95.5 - - + +
73R ARG* 1.3 57.5 + - - +
78R PHE* 3.5 13.5 - - + -
96R TYR* 4.3 10.1 - - + +
99R GLN* 3.4 38.8 - - + +
100R ILE* 3.7 43.7 - - + -
103R VAL* 3.7 22.7 - - + -
104R LYS* 3.0 31.4 + - - +
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Residues in contact with ARG 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R ASP 3.4 13.1 + - - +
70R GLN* 3.2 19.6 + - - +
71R TYR 3.1 0.4 - - - -
72R MET* 1.3 79.5 - - - +
74R THR* 1.3 81.4 + - - +
103R VAL* 3.6 13.0 - - + +
104R LYS* 2.8 20.5 + - - +
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Residues in contact with THR 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R LYS* 3.2 43.1 + - - +
7R VAL* 5.5 1.0 - - - +
56R LEU* 5.6 1.7 - - - +
70R GLN* 3.2 17.2 + - + +
71R TYR* 3.8 9.0 + - - +
73R ARG* 1.3 106.7 - - - +
75R GLY* 1.3 67.6 + - - +
76R GLU* 3.4 2.8 + - - +
104R LYS* 4.7 0.2 + - - -
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Residues in contact with GLY 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R LYS* 3.8 4.5 - - - -
7R VAL* 3.6 22.0 - - - -
71R TYR 2.9 17.7 + - - -
72R MET 4.1 0.2 + - - -
73R ARG 3.5 0.6 - - - -
74R THR* 1.3 78.7 + - - +
76R GLU* 1.3 60.4 + - - -
77R GLY 3.6 1.1 - - - -
78R PHE* 3.7 6.3 - - - -
104R LYS* 2.7 35.7 + - - -
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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