Contacts of the helix formed by residues 53 - 69 (chain C) in PDB entry 3UX9
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 ALA 53 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLU 4.9 2.4 + - - -
52C PRO* 1.3 72.4 - - - +
54C ILE* 1.3 64.7 + - - +
55C SER* 3.3 9.2 - - - +
56C VAL* 3.1 36.2 + - + +
57C LEU* 3.2 11.0 + - - +
113C ASN* 5.4 8.7 - - + -
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Residues in contact with ILE 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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52C PRO 3.6 2.6 + - - -
53C ALA* 1.3 67.1 - - - +
55C SER* 1.3 62.9 + - - +
56C VAL 2.9 5.8 - - - -
57C LEU* 3.1 13.0 + - + -
58C HIS* 2.8 34.7 + - - +
96C LEU* 3.4 46.9 - - + +
99C CYS* 3.6 29.4 - - + +
100C VAL* 4.0 16.2 - - + +
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ALA* 4.2 10.0 - - - +
54C ILE* 1.3 83.3 + - - +
56C VAL* 1.3 57.6 + - - +
58C HIS* 3.5 10.2 + - - +
59C GLU* 3.2 22.3 + - - +
100C VAL* 5.0 13.2 - - - +
113C ASN* 3.7 17.3 + - - -
117C ILE* 3.8 25.2 - - - +
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 4.4 13.2 - - + +
43C PHE* 3.9 28.9 - - + -
52C PRO 5.3 0.2 - - - -
53C ALA* 3.2 33.4 - - + +
55C SER* 1.3 83.3 - - - +
57C LEU* 1.3 69.5 + - + +
58C HIS 3.2 0.7 - - - -
59C GLU* 3.3 7.6 + - - +
60C LEU* 2.9 22.2 + - - +
113C ASN* 4.8 4.5 - - - +
116C SER* 4.5 19.3 - - - +
117C ILE* 4.3 14.8 - - + -
120C VAL* 4.7 8.8 - - + +
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 3.3 33.2 - - + -
43C PHE* 3.9 27.1 - - + -
52C PRO* 3.7 25.4 - - + +
53C ALA 3.2 18.5 + - - +
54C ILE* 3.1 20.4 + - + +
56C VAL* 1.3 81.3 - - - +
58C HIS* 1.3 64.8 + - - +
60C LEU* 3.1 7.3 + - + +
61C ILE* 3.0 28.6 + - - +
96C LEU* 4.5 3.1 - - + -
155C SER* 4.6 14.4 - - - +
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Residues in contact with HIS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE 2.8 16.9 + - - +
55C SER* 3.5 10.7 + - - +
57C LEU* 1.3 79.0 - - - +
59C GLU* 1.3 59.5 + - - +
61C ILE* 3.3 1.9 + - - +
62C GLN* 2.7 61.4 + - + +
93C LEU* 3.7 21.5 - - + +
96C LEU* 3.8 29.6 - - + +
97C GLU* 3.4 31.2 + - + +
100C VAL* 4.4 14.6 - - + +
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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
----------------------------------------------------------
55C SER 3.2 14.8 + - - +
56C VAL* 3.7 8.7 - - - +
57C LEU 3.2 0.4 - - - -
58C HIS* 1.3 86.9 + - - +
60C LEU* 1.3 58.3 + - - +
62C GLN* 3.4 14.1 - - - +
63C GLN* 2.8 65.1 + - + +
117C ILE* 3.6 40.1 - - + +
120C VAL* 4.3 12.8 - - + -
121C LYS* 3.6 15.3 + - + -
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 6.0 0.2 - - + -
38C PHE* 4.6 17.7 - - + -
43C PHE* 4.0 15.5 - - + -
56C VAL 2.9 14.0 + - - +
57C LEU* 3.1 13.2 + - + +
59C GLU* 1.3 75.0 - - - +
61C ILE* 1.3 68.9 + - + +
63C GLN* 3.1 4.5 + - - +
64C ILE* 3.0 37.2 + - + +
120C VAL* 4.1 9.8 - - + +
124C PHE* 3.8 26.9 - - + -
151C SER* 4.6 9.4 - - - +
152C LEU* 4.2 13.0 - - + -
155C SER* 3.6 33.7 - - - +
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Residues in contact with ILE 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.2 15.9 - - + -
57C LEU 3.0 14.5 + - - +
58C HIS 3.8 3.8 - - - +
60C LEU* 1.3 79.5 - - + +
62C GLN* 1.3 63.6 + - - +
64C ILE* 3.3 7.8 + - + +
65C PHE* 2.9 22.5 + - - +
89C LEU* 3.9 18.3 - - + +
92C GLN* 3.6 37.0 - - + +
93C LEU* 3.9 23.8 - - + -
96C LEU* 3.6 17.5 - - + -
152C LEU* 4.3 22.2 - - + -
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Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C HIS* 2.7 45.6 + - + +
59C GLU* 3.4 24.5 - - - +
61C ILE* 1.3 73.1 - - - +
63C GLN* 1.3 62.9 + - - +
65C PHE* 3.2 7.8 + - - +
66C ASN* 3.0 47.1 + - - +
93C LEU* 3.9 25.8 - - + +
97C GLU* 5.8 1.2 + - - -
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Residues in contact with GLN 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* 2.8 46.4 + - + +
62C GLN* 1.3 75.2 - - - +
64C ILE* 1.3 66.5 + - - +
66C ASN* 3.0 23.5 + - - +
67C LEU* 2.8 23.4 + - - +
120C VAL* 4.4 3.4 - - + +
121C LYS* 3.7 26.0 - - - +
124C PHE* 3.4 49.3 - - + +
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 3.0 27.8 + - + +
61C ILE* 3.6 11.4 - - + +
63C GLN* 1.3 74.5 - - - +
65C PHE* 1.3 62.3 + - - +
67C LEU* 3.2 6.5 + - - +
68C PHE* 3.1 34.2 + - + +
85C PHE* 4.3 5.4 - - + -
89C LEU* 4.0 23.3 - - + -
124C PHE* 3.6 21.8 - - + -
148C ILE* 3.7 29.2 - - + -
151C SER* 6.0 0.7 - - - -
152C LEU* 3.7 31.4 - - + +
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Residues in contact with PHE 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 ILE 2.9 17.3 + - - +
62C GLN* 3.4 11.4 - - - +
63C GLN 3.0 0.2 - - - -
64C ILE* 1.3 74.9 - - - +
66C ASN* 1.3 74.0 + - - +
68C PHE* 3.4 0.6 + - - -
69C THR* 2.9 59.3 + - + +
86C CYS* 3.8 18.8 - - + -
89C LEU* 3.9 30.0 - - + +
90C TYR* 4.5 23.3 - + + -
93C LEU* 4.2 16.2 - - + -
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Residues in contact with ASN 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 GLN* 3.0 35.8 + - - +
63C GLN* 3.5 30.0 + - - +
65C PHE* 1.3 83.2 - - - +
67C LEU* 1.3 64.9 + - - +
68C PHE 3.4 0.3 + - - -
69C THR* 3.5 13.7 + - - -
70C THR* 3.6 15.2 - - - +
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Residues in contact with LEU 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 GLN 2.8 13.5 + - - +
64C ILE* 3.3 10.1 - - - +
65C PHE 3.1 0.2 - - - -
66C ASN* 1.3 79.2 - - - +
68C PHE* 1.3 82.1 + - + +
70C THR* 3.3 23.1 + - + +
73C SER* 3.8 3.1 - - - -
124C PHE* 4.5 11.7 - - + -
127C ILE* 4.4 9.4 - - + -
128C THR* 4.3 23.6 - - + -
131C LEU* 4.4 18.8 - - + -
141C TRP* 4.4 7.8 - - + -
144C VAL* 4.2 16.6 - - + -
148C ILE* 4.3 15.9 - - + -
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Residues in contact with PHE 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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18C LEU* 4.2 15.5 - - + -
21C MET* 3.7 16.2 - - + -
64C ILE* 3.1 30.8 + - + +
65C PHE 3.4 1.3 + - - +
67C LEU* 1.3 99.4 - - + +
69C THR* 1.3 58.9 + - - +
70C THR 3.4 1.5 - - - +
73C SER* 2.6 28.5 + - - -
77C TRP* 3.5 33.4 - + - -
82C LEU* 3.9 19.2 - - + +
85C PHE* 3.9 16.6 - + + -
86C CYS* 3.8 15.1 - - - -
89C LEU* 5.0 1.1 - - + -
141C TRP* 4.3 10.8 - + - -
144C VAL* 4.7 1.3 - - + -
145C ARG* 4.5 14.4 - - - -
148C ILE* 4.0 14.8 - - + -
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Residues in contact with THR 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 PHE* 2.9 52.0 + - + +
66C ASN* 3.5 8.3 + - - -
67C LEU 3.4 0.4 - - - -
68C PHE* 1.3 80.9 - - - +
70C THR* 1.3 65.5 + - - +
86C CYS* 3.7 22.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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