Contacts of the strand formed by residues 12 - 21 (chain A) in PDB entry 1RKA
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 SER 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY* 1.3 73.3 - - - -
13A ILE* 1.3 60.6 - - - +
14A ASN* 4.3 4.5 - - - -
42A GLY* 3.9 3.0 - - - -
43A LYS 3.5 1.9 + - - -
44A GLY* 3.2 12.0 + - - -
45A ALA* 2.8 31.7 + - - +
117A ASN* 3.1 24.0 - - - -
141A GLN* 4.2 1.0 + - - -
143A GLU* 2.5 49.7 + - - +
144A SER* 3.8 2.6 + - - -
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Residues in contact with ILE 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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12A SER* 1.3 78.1 - - - +
14A ASN* 1.3 75.7 + - - +
41A GLY 4.0 4.0 - - - -
45A ALA* 4.2 5.8 - - + -
60A PHE* 3.6 21.5 - - + -
62A ALA* 3.6 24.0 - - + -
63A CYS 4.3 7.9 - - - +
64A THR* 3.7 24.0 - - + -
73A VAL* 3.7 34.8 - - + -
77A LEU* 4.1 11.9 - - + -
87A VAL* 4.1 6.5 - - + -
95A THR* 4.3 5.5 - - + +
96A GLY* 3.6 10.9 + - - -
117A ASN* 2.9 17.9 + - - +
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Residues in contact with ASN 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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12A SER* 4.7 2.7 - - - -
13A ILE* 1.3 92.8 + - - +
15A ALA* 1.3 58.6 - - - +
16A ASP* 3.6 15.7 - - - +
40A PHE* 3.7 6.4 - - - +
41A GLY 2.7 33.3 + - - +
42A GLY* 3.6 20.1 + - - +
73A VAL* 5.1 1.0 - - - +
95A THR* 5.2 1.6 - - - -
96A GLY* 3.3 16.5 - - - +
97A VAL* 3.9 8.9 - - - +
98A ALA* 4.3 4.9 - - - +
112A ILE* 4.3 23.8 - - - +
113A HIS 4.5 3.2 + - - -
117A ASN* 3.1 15.8 - - - +
143A GLU* 4.7 5.2 - - - +
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Residues in contact with ALA 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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14A ASN* 1.3 71.8 - - - +
16A ASP* 1.3 62.1 + - - +
17A HIS* 3.7 9.7 - - - +
38A VAL* 5.4 4.0 - - + -
39A ALA 4.1 2.7 - - - -
40A PHE* 4.7 8.3 - - + +
69A ILE* 3.7 34.5 - - + -
73A VAL* 6.5 0.4 - - + -
95A THR* 5.2 2.2 - - + -
96A GLY 3.0 13.8 + - - +
97A VAL* 3.4 17.0 - - + +
98A ALA 3.0 18.7 + - - -
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Residues in contact with ASP 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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14A ASN* 3.6 12.3 - - - +
15A ALA* 1.3 73.1 - - - +
17A HIS* 1.3 60.8 + - - +
18A ILE* 3.9 17.6 - - + +
37A GLN 3.4 1.9 - - - +
38A VAL* 3.2 7.9 - - - +
39A ALA* 2.7 49.5 + - + +
41A GLY* 3.4 18.1 - - - -
42A GLY 4.2 2.3 + - - -
46A ASN* 5.4 0.2 + - - -
98A ALA* 3.2 26.1 - - - +
100A ILE* 4.4 4.7 - - + -
251A ILE* 4.0 12.8 - - - +
291A ALA* 3.8 14.9 + - - +
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Residues in contact with HIS 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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15A ALA* 3.7 14.6 + - - +
16A ASP* 1.3 72.5 - - - +
18A ILE* 1.3 60.0 + - - +
19A LEU 4.1 0.2 + - - -
36A TYR* 2.9 32.2 + - + -
37A GLN 3.8 2.5 - - - -
38A VAL* 3.5 18.3 - - + +
69A ILE* 5.8 4.5 - - + +
97A VAL* 3.5 32.2 - - + +
98A ALA 2.8 7.7 + - - -
99A LEU* 3.7 18.3 - - + -
100A ILE* 2.8 29.1 + - - +
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Residues in contact with ILE 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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16A ASP* 4.2 17.9 - - + +
17A HIS* 1.3 77.1 - - - +
19A LEU* 1.3 64.0 + - - +
20A ASN* 4.2 9.3 + - - +
35A HIS 3.7 0.7 - - - +
36A TYR* 3.4 9.7 - - - -
37A GLN* 2.9 68.3 + - + +
39A ALA* 4.8 2.0 - - + -
100A ILE* 3.5 25.6 - - + +
102A VAL* 4.1 24.7 - - + -
249A ASP* 5.6 1.6 - - - +
251A ILE* 5.4 5.2 - - + -
290A GLY* 4.2 17.7 - - - +
291A ALA 5.1 1.6 - - - +
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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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17A HIS 4.1 0.8 + - - +
18A ILE* 1.3 75.0 - - - +
20A ASN* 1.3 71.2 + - - +
21A LEU* 3.8 9.5 + - + +
31A VAL* 5.1 5.6 - - + +
33A GLY* 4.0 24.0 - - - +
35A HIS 3.4 18.8 - - - +
36A TYR* 4.3 16.4 - - + -
100A ILE 2.8 13.1 + - - +
101A PHE* 3.4 27.7 - - + -
102A VAL 3.1 22.4 + - - -
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Residues in contact with ASN 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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18A ILE* 4.9 8.7 + - - +
19A LEU* 1.3 74.3 - - - +
21A LEU* 1.3 58.9 + - - +
33A GLY* 3.1 6.2 - - - -
34A ASN* 2.9 45.8 + - - +
35A HIS* 2.9 37.1 + - - +
37A GLN* 6.2 0.4 - - - +
102A VAL* 3.3 31.1 - - - +
103A ASN 5.4 0.2 - - - +
289A LYS* 5.8 5.9 - - - +
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Residues in contact with LEU 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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19A LEU* 4.1 11.4 - - + +
20A ASN* 1.3 77.6 - - - +
22A GLN* 1.3 66.0 + - - +
23A SER 3.5 22.2 - - - +
24A PHE* 3.9 8.3 - - + +
25A PRO* 3.9 12.3 - - + -
31A VAL* 3.5 32.3 - - + -
32A THR 4.6 1.6 - - - +
33A GLY* 4.0 14.4 - - - -
34A ASN* 3.8 10.3 + - - +
101A PHE* 4.1 24.9 - - + -
102A VAL 2.9 18.9 + - - +
103A ASN* 3.1 14.4 - - - -
104A GLY* 3.1 17.7 + - - -
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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