Contacts of the helix formed by residues 15 - 25 (chain A) in PDB entry 3R9X
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 GLY 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN 3.3 0.6 - - - -
14A VAL* 1.3 79.5 - - - +
16A LYS* 1.3 67.6 + - - +
17A SER 3.4 2.2 - - - -
18A THR* 3.1 2.9 + - - -
19A LEU* 2.9 23.9 + - - +
92A MET* 3.5 7.0 - - - +
123A ASN* 3.8 3.5 + - - -
402A GNP 3.1 38.8 + - - -
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Residues in contact with LYS 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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8A ILE* 3.4 39.8 - - + +
9A VAL* 3.5 22.7 - - - +
10A GLY* 3.3 8.9 + - - +
11A LYS 2.9 23.0 + - - -
14A VAL* 3.9 9.6 - - + -
15A GLY* 1.3 76.9 - - - +
17A SER* 1.3 64.1 + - - +
19A LEU* 3.1 3.6 + - - +
20A LEU* 3.0 20.8 + - - +
58A ASP* 3.2 15.3 - - - +
59A THR 3.5 16.2 - - - -
60A PRO 4.2 1.1 - - - -
61A GLY* 3.4 6.9 - - - -
92A MET* 3.5 8.9 - - - -
402A GNP 2.7 43.5 + - - +
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Residues in contact with SER 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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16A LYS* 1.3 72.2 - - - +
18A THR* 1.3 61.8 + - - +
20A LEU* 3.4 2.1 + - - +
21A ASN* 3.2 28.8 + - - +
29A SER* 3.0 10.2 + - - -
30A ILE 3.3 18.9 + - - -
31A ILE* 3.9 5.4 - - - -
38A THR* 2.8 4.5 + - - -
58A ASP* 2.3 28.3 + - - -
401A MG 2.3 28.7 - - - -
402A GNP 2.9 13.8 + - - -
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Residues in contact with THR 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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15A GLY 3.1 5.5 + - - -
17A SER* 1.3 73.3 - - - +
19A LEU* 1.3 63.7 + - - +
21A ASN* 3.3 1.4 + - - +
22A ASN* 2.8 35.7 + - - +
31A ILE* 3.5 19.6 - - + +
156A ALA* 3.6 30.1 - - + +
157A LEU* 3.7 15.7 - - + +
402A GNP 2.8 52.9 + - + +
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Residues in contact with LEU 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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8A ILE* 4.3 9.9 - - + -
15A GLY 2.9 11.8 + - - +
16A LYS 3.4 8.1 - - - +
18A THR* 1.3 77.4 - - - +
20A LEU* 1.3 62.9 + - - +
22A ASN* 3.2 2.1 + - - -
23A LEU* 2.9 50.4 + - + +
90A LEU* 4.2 15.0 - - + -
92A MET* 3.3 28.5 - - + -
121A VAL* 4.8 1.1 - - + -
154A ILE* 3.7 21.1 - - + -
156A ALA* 3.6 11.5 - - + +
162A LEU* 4.0 11.4 - - + -
165A LEU* 4.0 19.1 - - + -
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Residues in contact with LEU 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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8A ILE* 4.4 7.2 - - + +
16A LYS 3.0 13.0 + - - +
17A SER* 3.8 8.1 - - - +
18A THR 3.3 0.2 - - - -
19A LEU* 1.3 74.7 - - - +
21A ASN* 1.3 64.9 + - - +
23A LEU* 3.1 4.8 + - - +
24A LEU* 3.0 35.2 + - + +
28A VAL* 3.5 30.1 - - + -
29A SER* 4.3 1.8 - - - -
42A VAL* 3.7 16.6 - - + +
44A GLY 4.5 6.3 - - - +
56A PHE* 3.4 40.4 - - + -
58A ASP* 3.7 28.7 - - + +
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Residues in contact with ASN 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 SER 3.2 10.4 + - - +
18A THR 3.7 4.7 - - - +
19A LEU 3.2 0.2 - - - -
20A LEU* 1.3 80.4 - - - +
22A ASN* 1.3 63.4 + - - +
24A LEU* 4.9 0.4 - - - -
25A GLY* 2.8 22.3 + - - -
26A THR 3.2 19.4 + - - +
27A LYS* 3.3 17.7 - - + +
28A VAL* 3.0 27.4 + - - +
29A SER* 2.9 36.0 + - - -
31A ILE* 3.1 22.7 - - + +
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Residues in contact with ASN 22 (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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18A THR* 2.8 33.0 + - - +
19A LEU 4.2 1.1 - - - +
21A ASN* 1.3 82.3 - - - +
23A LEU* 1.3 64.6 + - - +
24A LEU 3.3 0.2 - - - -
25A GLY* 3.6 10.7 + - - +
156A ALA 3.2 25.8 + - - +
157A LEU* 3.9 10.6 + - - +
159A GLY* 4.7 7.1 + - - -
162A LEU* 4.0 20.5 - - + +
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Residues in contact with LEU 23 (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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8A ILE* 5.0 0.4 - - + -
19A LEU* 2.9 49.8 + - + +
20A LEU* 3.1 6.7 + - - +
22A ASN* 1.3 80.7 - - - +
24A LEU* 1.3 61.2 + - - +
46A LYS* 3.0 33.8 + - + +
56A PHE* 3.6 41.7 - - + -
162A LEU* 4.3 20.6 - - + +
165A LEU* 4.3 10.3 - - + -
166A VAL* 3.7 28.9 - - + -
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Residues in contact with LEU 24 (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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20A LEU* 3.0 19.5 + - + +
23A LEU* 1.3 80.3 - - - +
25A GLY* 1.3 62.2 + - - +
26A THR* 4.0 16.8 - - - +
28A VAL* 3.5 34.3 - - + -
44A GLY* 3.7 25.8 - - - +
45A VAL 3.6 22.7 - - - +
46A LYS* 3.7 26.6 + - + +
56A PHE* 4.5 6.5 - - + -
185A ILE* 3.9 15.8 - - + +
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Residues in contact with GLY 25 (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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21A ASN 2.8 9.4 + - - -
22A ASN* 3.6 9.7 + - - -
23A LEU 3.4 2.8 - - - -
24A LEU* 1.3 79.1 - - - +
26A THR* 1.3 64.9 + - - +
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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