Contacts of the helix formed by residues 11 - 21 (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 ASN 11 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C LEU* 3.5 18.3 + - - +
10C ASP* 1.3 72.3 + - - +
12C ARG* 1.3 68.6 + - - +
13C ARG 3.3 1.8 - - - -
14C THR* 3.0 13.3 + - - +
15C LEU* 2.8 37.1 + - + +
61C ILE* 4.5 0.5 - - - +
92C GLN* 3.0 21.1 + - - -
152C LEU* 3.3 46.0 + - + +
155C SER* 3.5 7.7 + - - -
156C THR* 3.4 22.6 - - + +
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Residues in contact with ARG 12 (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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10C ASP* 2.2 51.0 + - - +
11C ASN* 1.3 82.9 - - - +
13C ARG* 1.3 58.6 - - - +
15C LEU* 3.1 8.6 + - - +
16C MET* 2.9 35.7 + - - +
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASP* 4.4 9.7 + - - +
11C ASN 3.3 0.2 - - - -
12C ARG* 1.3 75.7 - - - +
14C THR* 1.3 66.1 + - - +
16C MET* 3.2 35.8 + - - +
17C LEU* 3.0 41.6 + - + +
88C GLU* 3.6 39.1 + - + +
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Residues in contact with THR 14 (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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10C ASP 5.0 0.4 + - - +
11C ASN* 2.9 35.2 + - - +
13C ARG* 1.3 78.5 - - - +
15C LEU* 1.3 62.5 + - - +
17C LEU* 3.2 4.0 + - - +
18C LEU* 2.9 27.0 + - - +
85C PHE* 3.7 24.9 - - + -
88C GLU* 3.8 21.3 - - + -
89C LEU* 4.0 10.5 - - + -
92C GLN* 3.7 22.9 - - - +
152C LEU* 4.1 11.4 - - + +
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Residues in contact with LEU 15 (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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11C ASN* 2.8 37.1 + - + +
12C ARG* 3.4 6.3 - - - +
14C THR* 1.3 77.9 - - - +
16C MET* 1.3 62.1 + - + +
18C LEU* 3.3 4.8 + - + +
19C ALA* 3.0 23.4 + - - +
149C MET* 3.4 54.5 - - + +
152C LEU* 3.7 11.9 - - + -
153C SER* 4.2 22.9 - - - -
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Residues in contact with MET 16 (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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12C ARG* 2.9 22.2 + - + +
13C ARG* 3.4 34.8 - - - +
14C THR 3.2 0.2 - - - -
15C LEU* 1.3 73.5 - - + +
17C LEU* 1.3 66.7 + - - +
19C ALA* 3.2 8.2 + - - +
20C GLN* 3.0 25.7 + - - +
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Residues in contact with LEU 17 (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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13C ARG* 3.0 43.4 + - + +
14C THR* 3.6 6.1 - - - +
16C MET* 1.3 76.5 - - + +
18C LEU* 1.3 63.5 + - - +
20C GLN* 3.1 10.0 + - - +
21C MET* 2.9 30.2 + - + +
81C LEU* 4.4 15.2 - - + +
84C LYS* 3.9 34.3 - - + +
85C PHE* 3.5 41.3 - - + +
88C GLU* 4.5 3.8 - - + -
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Residues in contact with LEU 18 (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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14C THR 2.9 12.8 + - - +
15C LEU* 3.5 5.4 - - - +
16C MET 3.1 0.2 - - - -
17C LEU* 1.3 75.9 - - - +
19C ALA* 1.3 64.4 + - - +
21C MET* 3.0 26.7 + - + +
68C PHE* 4.2 11.4 - - + -
85C PHE* 3.4 30.1 - - + -
145C ARG* 3.0 43.8 - - + +
148C ILE* 3.7 26.7 - - + -
149C MET* 3.6 23.1 - - + +
152C LEU* 3.8 18.8 - - + -
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Residues in contact with ALA 19 (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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15C LEU 3.0 11.2 + - - +
16C MET* 3.7 7.0 - - - +
18C LEU* 1.3 77.3 - - - +
20C GLN* 1.3 59.5 + - - +
22C SER* 3.8 15.4 - - - -
145C ARG* 3.7 11.8 + - - +
149C MET* 3.7 19.2 - - + -
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Residues in contact with GLN 20 (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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16C MET* 3.0 15.5 + - - +
17C LEU* 3.7 9.4 - - - +
18C LEU 3.0 0.8 - - - -
19C ALA* 1.3 77.5 - - - +
21C MET* 1.3 59.7 + - - +
22C SER 3.0 11.5 + - - +
81C LEU* 3.5 30.7 - - + +
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Residues in contact with MET 21 (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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17C LEU* 2.9 20.1 + - - +
18C LEU* 3.0 19.1 + - + +
20C GLN* 1.3 75.2 - - - +
22C SER* 1.3 65.2 + - - +
23C ARG* 3.4 6.4 + - - +
68C PHE* 3.7 24.5 - - + -
77C TRP* 3.1 58.4 - - + -
78C ASP* 5.5 2.4 + - - +
81C LEU* 3.9 27.8 - - + +
82C LEU* 4.3 7.9 - - + +
85C PHE* 4.0 31.4 - - - -
145C ARG* 4.1 3.1 - - + -
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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