Contacts of the helix formed by residues 11 - 21 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.7 12.7 + - - +
10A ASP* 1.3 81.2 + - - +
12A ARG* 1.3 63.2 + - - +
14A THR* 2.8 23.9 + - - +
15A LEU* 2.9 30.6 + - + +
61A ILE* 4.6 3.3 - - - +
92A GLN* 3.6 12.6 - - - +
152A LEU* 2.0 58.5 - - + +
155A SER* 4.1 3.7 + - - -
156A THR* 4.4 10.2 - - + +
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Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 2.5 38.3 + - - +
11A ASN* 1.3 77.9 - - - +
13A ARG* 1.3 57.8 + - - +
15A LEU* 3.0 6.0 + - - +
16A MET* 2.9 35.3 + - - +
145D LEU* 4.1 25.7 - - + +
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 4.4 5.3 + - - +
12A ARG* 1.3 79.4 - - - +
14A THR* 1.3 60.9 + - - +
16A MET* 3.3 34.8 + - - +
17A LEU* 3.0 41.8 + - + +
88A GLU* 3.6 38.7 + - + +
248D LEU* 5.2 4.2 - - - +
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Residues in contact with THR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP 4.6 0.2 + - - -
11A ASN* 2.8 34.8 + - - +
13A ARG* 1.3 76.9 - - - +
15A LEU* 1.3 61.1 + - - +
17A LEU* 3.2 3.0 + - - -
18A LEU* 2.9 27.9 + - - +
85A PHE* 3.7 18.2 - - + -
88A GLU* 3.9 20.4 - - + -
89A LEU* 4.0 16.2 - - + -
92A GLN* 3.7 23.9 + - - +
152A LEU* 3.9 14.2 - - + +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN* 2.9 35.4 + - + +
12A ARG* 3.3 4.3 - - + +
14A THR* 1.3 76.2 - - - +
16A MET* 1.3 61.7 + - - +
18A LEU* 3.3 4.5 + - - +
19A ALA* 3.0 24.0 + - - +
149A MET* 3.4 54.9 - - + +
152A LEU* 3.7 13.2 - - + -
153A SER* 4.2 23.8 - - - -
145D LEU* 4.1 23.3 - - + -
250D THR* 5.4 1.3 - - - -
254D LEU* 5.4 4.3 - - + -
255D GLU 4.6 9.9 - - - +
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Residues in contact with MET 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG* 2.9 19.6 + - - +
13A ARG* 3.4 34.8 - - - +
15A LEU* 1.3 73.0 - - - +
17A LEU* 1.3 67.4 + - - +
19A ALA* 3.1 5.0 + - - +
20A GLN* 3.1 21.7 + - - +
143D GLY 5.6 0.2 - - - -
144D GLY* 3.7 29.6 - - - +
145D LEU* 4.1 12.8 - - + -
248D LEU* 3.4 45.4 - - + +
250D THR* 3.5 25.8 + - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.0 45.3 + - + +
14A THR* 3.7 4.3 - - - +
16A MET* 1.3 75.2 - - + +
18A LEU* 1.3 55.6 + - - +
20A GLN* 3.1 7.1 + - - +
21A MET* 3.0 35.8 + - + +
81A LEU* 4.6 15.7 - - + +
84A LYS* 3.9 34.1 - - + +
85A PHE* 3.6 41.1 - - + +
88A GLU* 4.6 4.0 - - + -
248D LEU* 4.7 8.3 - - + -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR 2.9 12.1 + - - +
15A LEU* 3.5 5.8 - - - +
16A MET 3.1 0.2 - - - -
17A LEU* 1.3 72.7 - - - +
19A ALA* 1.3 65.0 + - - +
20A GLN 3.0 1.3 - - - -
21A MET* 3.1 21.4 + - + +
68A PHE* 4.2 11.0 - - + -
85A PHE* 3.3 35.2 - - + -
145A ARG* 3.0 48.7 - - + +
148A ILE* 3.7 27.8 - - + -
149A MET* 3.6 23.1 - - + +
152A LEU* 3.8 14.8 - - + -
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU 3.0 10.3 + - - +
16A MET 3.1 5.4 + - - +
18A LEU* 1.3 76.9 - - - +
20A GLN* 1.3 60.5 + - - +
22A SER* 3.8 9.5 + - - -
145A ARG* 3.7 11.7 + - - +
149A MET* 3.8 12.5 - - + -
175D PRO* 3.4 18.3 - - - +
225D THR* 4.7 6.0 - - + +
250D THR* 3.4 34.1 - - + +
252D SER* 6.0 0.2 - - - -
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET 3.1 10.7 + - - +
17A LEU* 3.5 9.6 - - - +
18A LEU 3.0 0.8 - - - -
19A ALA* 1.3 76.7 - - - +
21A MET* 1.3 58.5 + - - +
22A SER 3.0 9.1 + - - +
81A LEU* 3.3 29.6 - - + +
173D GLN 3.8 9.1 + - - -
174D ALA 3.7 3.2 - - - -
175D PRO* 3.1 52.5 - - + +
176D GLY 4.8 0.9 + - - -
225D THR* 4.7 1.0 - - - +
226D ALA* 4.0 3.9 + - - +
227D VAL* 4.1 13.0 - - + +
248D LEU* 2.4 45.7 - - + +
250D THR* 4.6 1.2 + - - -
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Residues in contact with MET 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU 3.0 19.2 + - - +
18A LEU* 3.1 21.2 + - + +
20A GLN* 1.3 75.6 - - - +
22A SER* 1.3 65.4 + - - +
23A ARG* 3.5 6.2 + - - +
68A PHE* 3.7 24.9 - - + -
77A TRP* 3.0 58.8 - - + -
78A ASP* 5.5 2.4 + - - +
81A LEU* 3.8 28.3 - - + +
82A LEU* 4.3 8.5 - - + +
85A PHE* 4.0 31.2 - - - -
145A ARG* 4.1 2.5 - - + -
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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