Contacts of the helix formed by residues 76 - 89 (chain B) in PDB entry 1RJJ
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 HIS 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B GLN* 2.6 48.6 + - + +
35B ASP* 5.7 3.8 + - - -
72B ALA* 3.5 9.4 + - + -
73B PHE 4.2 5.0 - - - +
74B THR 2.7 17.2 + - - +
75B SER* 1.3 89.5 + - - +
77B PRO* 1.3 72.0 - - + +
78B LEU* 3.2 11.6 + - + +
79B HIS* 3.7 9.2 + - - +
80B VAL* 4.3 6.2 + - - +
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Residues in contact with PRO 77 (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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75B SER 4.6 1.3 - - - +
76B HIS* 1.3 92.2 - - + +
78B LEU* 1.3 63.2 + - + +
79B HIS 3.3 0.8 + - - -
80B VAL* 4.0 9.8 - - + +
81B GLU* 3.4 28.2 + - - +
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Residues in contact with LEU 78 (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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29B ASN* 3.0 49.1 - - - +
30B LEU* 3.6 31.3 - - + +
32B SER* 4.7 3.4 - - - -
33B GLN* 4.7 11.7 - - + +
76B HIS* 3.2 10.7 - - + -
77B PRO* 1.3 83.8 - - + +
79B HIS* 1.3 58.8 + - - +
81B GLU* 3.4 20.4 - - - +
82B PHE* 3.0 26.5 + - - +
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Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.8 0.4 - - - -
33B GLN* 6.2 0.2 - - - +
62B MET* 6.5 0.9 - - + -
73B PHE* 2.9 70.0 + + + +
74B THR* 4.6 11.9 - - - -
76B HIS 3.7 4.9 + - - +
77B PRO 3.3 0.6 - - - -
78B LEU* 1.3 78.5 - - - +
80B VAL* 1.3 60.8 + - + +
82B PHE* 4.3 8.0 - + - -
83B SER* 2.6 55.4 + - - -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 5.3 4.5 - - - +
76B HIS 4.3 10.7 + - - +
77B PRO* 3.7 10.3 + - + +
78B LEU 3.4 0.2 - - - -
79B HIS* 1.3 82.0 - - + +
81B GLU* 1.3 66.8 + - - +
83B SER* 3.1 6.0 + - - -
84B ALA* 3.0 23.9 + - + +
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Residues in contact with GLU 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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77B PRO* 3.4 16.5 + - - +
78B LEU* 3.4 34.2 - - - +
80B VAL* 1.3 82.4 - - + +
82B PHE* 1.3 76.4 + - + +
84B ALA* 3.5 7.3 + - - +
85B ALA* 3.5 17.7 + - - +
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Residues in contact with PHE 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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23B ILE* 4.3 19.5 - - + -
26B GLY* 4.6 19.5 - - - -
27B LEU* 4.3 25.4 - - + -
29B ASN* 5.4 5.8 - - - +
30B LEU* 4.4 21.3 - - + -
62B MET* 6.4 2.5 - - + -
73B PHE* 5.9 0.4 - + - -
78B LEU* 3.0 20.4 + - + +
79B HIS* 3.8 9.2 - + - +
80B VAL 3.1 0.4 - - - -
81B GLU* 1.3 83.2 - - + +
83B SER* 1.3 55.8 + - - +
85B ALA* 3.2 9.8 + - + +
86B PHE* 2.7 66.0 + + + +
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Residues in contact with SER 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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79B HIS* 2.6 44.8 + - - -
80B VAL* 3.6 6.1 - - - -
82B PHE* 1.3 75.4 - - - +
84B ALA* 1.3 64.7 + - - +
86B PHE* 3.1 15.4 + - - +
87B THR* 2.9 23.1 + - - +
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Residues in contact with ALA 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 VAL* 3.0 13.8 + - + +
81B GLU* 3.7 11.4 - - - +
82B PHE 3.2 0.2 - - - -
83B SER* 1.3 77.3 - - - +
85B ALA* 1.3 59.6 + - - +
87B THR* 2.8 30.0 + - - -
88B ALA* 3.3 4.2 + - - +
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Residues in contact with ALA 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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81B GLU 3.5 8.5 + - - +
82B PHE* 3.2 12.6 + - + +
84B ALA* 1.3 74.3 - - - +
86B PHE* 1.3 68.6 + - - +
87B THR 2.6 6.5 + - - -
88B ALA* 2.9 11.1 + - + -
89B VAL* 2.8 28.2 + - + +
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Residues in contact with PHE 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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10B VAL* 4.1 13.9 - - + -
12B VAL* 4.2 5.4 - - + -
23B ILE* 5.4 5.8 - - + -
60B PHE* 3.6 41.1 - + - -
62B MET* 6.0 4.5 - - + -
82B PHE* 2.7 49.9 + + - +
83B SER* 3.3 18.2 - - - +
85B ALA* 1.3 72.7 - - - +
87B THR* 1.3 59.9 + - + +
89B VAL* 3.2 10.1 - - + +
90B ILE* 2.8 44.2 - - + +
93B ILE* 3.5 32.5 - - + -
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Residues in contact with THR 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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83B SER* 2.9 21.5 - - - +
84B ALA* 2.8 13.2 + - - +
85B ALA 2.6 3.6 + - - -
86B PHE* 1.3 74.6 - - + +
88B ALA* 1.3 70.4 + - - +
89B VAL 2.5 4.9 + - - -
90B ILE* 2.4 42.0 + - - +
93B ILE* 6.1 2.2 - - + -
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Residues in contact with ALA 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 LYS* 6.0 0.2 - - - -
16B GLU* 3.1 30.0 - - - +
84B ALA 3.3 3.3 + - - +
85B ALA* 2.9 19.8 + - + +
87B THR* 1.3 82.1 + - - +
89B VAL* 1.3 56.9 + - + +
90B ILE 3.3 2.0 + - - +
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Residues in contact with VAL 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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14B PHE* 4.9 0.2 - - - +
15B LYS 6.2 0.2 - - - -
16B GLU* 4.4 11.2 - - + +
17B ASP 5.4 0.4 - - - -
18B THR* 2.8 43.4 + - + -
19B LYS* 3.7 29.8 - - - -
23B ILE* 4.1 21.8 - - + -
85B ALA* 2.8 14.5 + - + +
86B PHE* 3.2 25.6 - - + +
87B THR 2.5 8.9 + - - -
88B ALA* 1.3 75.8 - - + +
90B ILE* 1.3 60.5 + - + +
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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