Contacts of the helix formed by residues 15 - 26 (chain B) in PDB entry 1RYF
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ALA 3.2 1.0 - - - -
14B VAL* 1.3 80.9 - - - +
16B LYS* 1.3 60.3 + - - +
18B CYS* 3.8 1.2 - - - +
19B LEU* 2.9 31.4 + - - +
134B THR* 5.0 7.0 - - - +
178B ALA* 5.1 0.3 - - - +
1538B GDP 3.0 43.6 + - - -
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.0 20.0 - - + +
9B VAL* 3.5 32.8 - - - +
10B GLY* 3.1 13.9 + - - +
11B ASP 2.9 23.0 + - - -
12B GLY* 3.9 3.0 - - - -
14B VAL* 3.7 12.8 - - + -
15B GLY* 1.3 73.2 - - - +
17B THR* 1.3 60.8 + - - +
19B LEU* 3.4 7.3 + - - +
20B LEU* 3.2 28.8 + - - +
57B ASP* 3.9 11.9 - - - +
58B THR* 3.9 26.4 + - - -
100B CYS* 4.2 7.4 - - + -
1538B GDP 2.8 40.4 + - - +
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS* 1.3 75.6 - - - +
18B CYS* 1.3 57.6 + - - +
20B LEU* 3.3 4.8 + - - +
21B ILE* 2.9 38.3 + - + +
33B ILE* 3.8 37.2 - - + +
40B TYR* 4.0 3.8 - - - +
57B ASP* 2.5 26.8 + - - +
1538B GDP 3.0 13.2 + - - +
1539B MG 2.1 30.4 - - - -
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Residues in contact with CYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY 3.9 0.7 - - - +
17B THR* 1.3 71.6 - - - +
19B LEU* 1.3 60.3 + - - +
22B SER* 2.8 35.3 + - - -
28B PHE* 3.7 21.3 - - + -
29B PRO* 3.7 29.0 - - - +
33B ILE* 6.3 0.7 - - - -
178B ALA* 3.8 2.0 - - + -
1538B GDP 2.8 64.5 + - + +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.6 2.7 - - + -
15B GLY 2.9 23.4 + - - +
16B LYS* 3.5 5.8 - - - +
18B CYS* 1.3 70.5 - - - +
20B LEU* 1.3 63.1 + - + +
22B SER* 4.0 0.2 - - - -
23B TYR* 3.0 31.9 + - - +
98B LEU* 4.1 17.9 - - + -
100B CYS* 4.1 20.0 - - - -
132B VAL* 4.9 3.1 - - + -
134B THR* 4.8 6.3 - - + -
176B CYS* 3.4 24.9 - - - -
178B ALA* 3.7 13.1 - - + +
184B LEU* 3.2 31.7 - - + +
187B VAL* 4.9 4.3 - - + -
188B PHE* 3.9 22.0 - - + -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.9 29.8 - - + -
16B LYS 3.2 17.0 + - - +
17B THR 3.7 3.6 - - - +
18B CYS 3.3 0.2 - - - -
19B LEU* 1.3 80.3 - - + +
21B ILE* 1.3 59.3 + - - +
23B TYR* 3.5 2.9 + - - +
24B THR* 2.9 36.0 + - - +
40B TYR* 3.8 22.0 - - + -
55B LEU* 4.0 19.5 - - + -
57B ASP* 3.6 38.6 - - + +
188B PHE* 3.9 25.4 - - + -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 5.3 5.8 - - + -
37A PHE* 3.9 12.3 - - + -
17B THR* 2.9 21.9 + - + +
18B CYS 4.2 0.2 - - - +
20B LEU* 1.3 73.4 - - - +
22B SER* 1.3 67.1 + - - +
24B THR* 3.9 4.7 - - - -
25B THR* 2.8 45.0 + - + +
27B ALA 3.8 12.3 - - - +
29B PRO* 3.9 21.8 - - + -
33B ILE* 3.7 35.9 - - + -
40B TYR* 3.5 36.6 - - + +
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B CYS 2.8 20.0 + - - -
21B ILE* 1.3 76.5 - - - +
23B TYR* 1.3 58.9 + - - +
26B ASN 3.0 21.7 + - - -
27B ALA 3.3 15.0 - - - -
28B PHE* 3.9 10.7 + - - -
29B PRO* 4.6 0.2 - - - +
178B ALA* 2.8 31.2 + - - -
181B GLN* 3.0 30.9 + - - +
184B LEU* 3.5 9.3 - - - +
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU 3.0 19.0 + - - +
20B LEU 3.8 2.5 - - - +
22B SER* 1.3 79.5 - - - +
24B THR* 1.3 72.1 + - + +
26B ASN* 3.9 11.3 + - - +
42B ALA* 4.0 18.6 - - + -
44B VAL* 3.3 31.8 - - + +
53B LEU* 4.2 7.6 - - + +
55B LEU* 4.2 3.1 - - + -
181B GLN* 4.8 0.4 - - - +
184B LEU* 3.6 13.2 - - + +
185B LYS* 4.1 38.2 + - + -
188B PHE* 3.4 62.3 - + + +
189B ASP* 4.8 4.9 + - - -
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN* 5.3 4.2 + - - +
20B LEU 2.9 24.2 + - - +
21B ILE* 3.7 4.3 + - - -
23B TYR* 1.3 82.7 - - + +
25B THR* 1.3 68.7 + - - +
26B ASN* 5.4 2.0 + - - -
40B TYR* 3.9 27.3 - - + +
41B SER 3.5 27.7 - - - +
42B ALA* 4.3 6.1 - - + +
55B LEU* 3.9 19.1 - - + -
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.4 23.0 - - - +
37A PHE* 4.5 13.9 - - + -
21B ILE* 2.8 36.0 + - + +
24B THR* 1.3 85.3 - - - +
26B ASN* 1.3 69.5 + - - +
27B ALA* 3.0 27.4 + - - +
40B TYR* 6.1 0.4 - - + -
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Residues in contact with ASN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER 3.0 12.8 + - - -
23B TYR 3.9 6.3 + - - +
24B THR 3.6 3.0 + - - -
25B THR* 1.3 78.9 + - - +
27B ALA* 1.3 58.9 + - - +
181B GLN* 3.5 31.2 + - - +
185B LYS* 3.8 22.7 + - - +
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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