Contacts of the helix formed by residues 79 - 92 (chain B) in PDB entry 1RX0
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 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLN* 4.6 1.2 + - - -
68B TYR* 5.0 0.9 - - - -
78B LEU* 1.3 71.7 - - - +
80B ARG* 1.3 60.5 + - - +
81B LEU* 4.1 2.1 - - - +
82B ASP* 2.9 39.1 + - - -
83B THR* 2.8 33.1 + - - -
319B GLN* 3.3 23.9 + - - -
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Residues in contact with ARG 80 (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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68B TYR* 3.7 34.2 + - - -
79B SER* 1.3 75.4 - - - +
81B LEU* 1.3 63.2 + - - +
83B THR* 3.3 7.4 + - - -
84B SER* 3.0 22.2 + - - -
109B TRP* 3.5 37.2 - - - +
249B ARG* 4.8 6.3 + - - +
252B ASN* 5.9 0.2 - - - +
253B GLY* 3.7 20.5 - - - -
256B ILE* 4.8 6.5 - - + +
257B ASN* 4.9 2.5 - - - +
315B ALA* 3.5 25.8 - - + +
318B LEU* 3.6 30.3 - - + +
319B GLN* 3.2 27.2 + - + +
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Residues in contact with LEU 81 (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 GLY 6.1 0.7 - - - +
19B LEU* 4.6 6.1 - - + -
23B GLN* 3.4 28.9 - - - +
79B SER* 4.1 0.9 - - - +
80B ARG* 1.3 72.3 - - - +
82B ASP* 1.3 66.6 + - - +
84B SER* 3.1 4.3 + - - -
85B VAL* 3.0 29.8 + - + +
312B ARG* 3.7 46.9 - - + +
315B ALA* 3.9 10.0 - - + +
316B VAL* 3.9 20.0 - - + -
319B GLN* 2.9 21.6 + - - +
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Residues in contact with ASP 82 (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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20B ASN* 5.0 0.5 + - - -
22B GLU* 5.5 1.4 - - - +
23B GLN* 2.9 37.2 + - - +
26B PHE* 3.9 19.3 - - + -
78B LEU* 3.6 26.0 - - + +
79B SER* 2.9 36.4 + - - +
81B LEU* 1.3 78.2 - - - +
83B THR* 1.3 64.1 + - - +
85B VAL* 3.4 6.1 + - - +
86B ILE* 3.0 28.9 + - - +
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Residues in contact with THR 83 (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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67B VAL* 3.4 24.4 - - + +
68B TYR* 3.4 30.6 - - + +
78B LEU 4.5 0.2 + - - -
79B SER 2.8 21.4 + - - -
80B ARG* 3.5 7.6 - - - -
82B ASP* 1.3 74.7 - - - +
84B SER* 1.3 60.4 + - - +
86B ILE* 3.3 1.8 + - - +
87B PHE* 2.9 60.6 + - + -
257B ASN* 3.5 12.1 - - - +
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Residues in contact with SER 84 (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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80B ARG 3.0 13.2 + - - -
81B LEU* 3.5 15.3 - - - -
83B THR* 1.3 76.6 - - - +
85B VAL* 1.3 58.5 + - - +
88B GLU* 2.9 32.8 + - - +
256B ILE* 4.2 11.9 - - - -
257B ASN* 4.4 4.0 + - - -
260B SER* 2.7 29.4 + - - -
263B LEU* 5.0 2.6 - - - +
311B VAL* 3.5 13.7 - - - +
312B ARG* 4.7 8.8 + - - +
315B ALA* 4.6 4.3 - - - -
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Residues in contact with VAL 85 (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* 3.7 35.4 - - + -
23B GLN* 4.1 11.4 - - + +
26B PHE* 5.2 0.9 - - + -
27B GLN* 3.6 42.6 - - + +
81B LEU* 3.0 21.7 + - + +
82B ASP* 3.6 9.6 - - - +
84B SER* 1.3 75.9 - - - +
86B ILE* 1.3 63.3 + - + +
88B GLU* 3.5 10.1 + - - +
89B ALA* 3.1 22.3 + - - +
312B ARG* 4.3 13.2 - - - +
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Residues in contact with ILE 86 (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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26B PHE* 4.1 27.6 - - + +
30B ALA* 3.9 6.5 - - + +
64B PHE* 3.8 40.2 - - + -
67B VAL* 3.8 13.9 - - + -
78B LEU* 3.6 31.2 - - + -
82B ASP 3.0 16.6 + - - +
83B THR* 3.3 5.4 + - - +
85B VAL* 1.3 74.8 - - + +
87B PHE* 1.3 68.7 + - + +
89B ALA* 3.2 4.2 + - - +
90B LEU* 2.9 41.7 + - + +
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Residues in contact with PHE 87 (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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64B PHE 4.9 0.2 - - - -
67B VAL* 4.1 18.6 - - + -
68B TYR* 4.6 1.3 - + - -
83B THR* 2.9 37.4 + - + +
84B SER 4.1 2.0 - - - +
86B ILE* 1.3 78.8 - - + +
88B GLU* 1.3 60.5 + - - +
90B LEU* 4.3 5.6 - - + -
91B ALA* 2.9 31.9 + - - +
98B THR* 3.4 22.3 - - + +
101B ILE* 4.2 17.3 - - + -
102B SER* 3.4 36.3 - - - -
105B ASN* 4.1 17.0 - - + -
257B ASN* 3.6 29.8 - - + -
260B SER* 4.3 12.6 - - - -
261B CYS* 4.5 4.7 - - - -
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Residues in contact with GLU 88 (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 PRO* 5.1 1.3 - - - -
27B GLN* 4.6 2.4 - - - +
84B SER* 2.9 17.6 + - - +
85B VAL* 3.7 9.0 - - - +
86B ILE 3.3 0.2 - - - -
87B PHE* 1.3 77.1 - - - +
89B ALA* 1.3 63.5 + - - +
91B ALA 3.4 3.8 + - - -
92B THR* 3.5 4.0 - - - +
260B SER* 3.4 19.4 + - - +
263B LEU* 3.6 20.3 - - + +
264B GLY* 3.3 36.2 - - - +
308B ARG* 2.8 39.8 + - - -
312B ARG* 2.9 27.8 + - - -
2006B EDO 4.1 11.7 - - - +
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Residues in contact with ALA 89 (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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27B GLN* 3.9 12.6 - - + +
30B ALA* 3.7 19.5 - - + -
31B PHE* 3.8 11.3 - - - +
34B ALA* 3.7 7.8 - - - +
85B VAL 3.1 11.9 + - - +
86B ILE 3.6 7.4 - - - +
88B GLU* 1.3 81.4 - - - +
90B LEU* 1.3 57.0 + - - +
92B THR* 2.6 26.7 + - - -
2006B EDO 3.9 22.0 - - - -
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Residues in contact with LEU 90 (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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30B ALA* 3.6 22.2 - - + +
33B PHE* 3.9 23.6 - - + -
34B ALA* 3.9 3.2 - - - +
38B MET* 3.6 13.9 - - - +
59B ALA* 5.8 0.2 - - + -
64B PHE* 4.0 28.0 - - + -
86B ILE* 2.9 35.3 + - + +
87B PHE* 4.3 14.1 - - + -
89B ALA* 1.3 76.0 - - - +
91B ALA* 1.3 57.8 + - - +
92B THR 3.1 0.2 - - - -
93B GLY* 2.9 19.2 + - - -
94B CYS 3.3 6.1 + - - -
98B THR* 3.1 24.3 + - + +
101B ILE* 4.7 14.4 - - + -
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Residues in contact with ALA 91 (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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87B PHE 2.9 17.3 + - - +
88B GLU 3.7 6.5 - - - +
89B ALA 3.3 0.4 - - - -
90B LEU* 1.3 76.6 - - - +
92B THR* 1.3 62.3 + - - +
93B GLY 3.1 0.8 + - - -
94B CYS 3.6 4.8 + - - -
95B THR* 3.0 33.8 + - - +
98B THR* 3.2 9.8 + - - -
261B CYS* 3.4 36.3 - - + +
264B GLY* 4.0 4.5 - - - -
265B ALA 4.3 1.2 + - - -
365B TYR* 3.9 4.9 - - - -
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Residues in contact with THR 92 (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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31B PHE* 3.6 23.2 - - + -
34B ALA* 4.1 3.3 - - - +
39B ALA* 5.0 3.6 - - - +
88B GLU 3.5 14.6 - - - +
89B ALA 2.6 18.2 + - - +
91B ALA* 1.3 76.7 - - - +
93B GLY* 1.3 58.2 + - - +
264B GLY* 3.5 23.8 - - - +
267B HIS* 4.9 2.9 - - + +
268B ALA* 4.2 16.0 - - + +
365B TYR* 2.7 24.2 + - - -
2006B EDO 4.0 20.6 - - - +
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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