Contacts of the helix formed by residues 80 - 96 (chain B) in PDB entry 4RPP
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 THR 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLY* 1.3 75.3 - - - -
81B HIS* 1.3 61.6 + - - +
82B GLU* 3.4 13.5 + - - +
83B TYR* 3.1 23.2 + - - +
84B HIS* 3.0 33.2 + - - -
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Residues in contact with HIS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 4.2 6.5 - + - -
79B GLY 5.8 0.4 - - - -
80B THR* 1.3 73.1 - - - +
82B GLU* 1.3 60.1 + - - +
84B HIS* 4.7 0.2 - - - -
85B ALA* 2.8 35.4 + - - +
224B LYS* 5.8 0.6 - - - -
227B GLN* 3.9 23.3 - - + -
228B ASP* 2.9 28.1 + - - -
231B PHE* 3.5 53.6 - + + +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 3.2 11.0 + - - +
81B HIS* 1.3 80.6 - - - +
83B TYR* 1.3 64.0 + - - +
85B ALA* 3.9 4.7 - - - +
86B GLU* 3.4 18.5 + - - +
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Residues in contact with TYR 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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51B ILE 5.7 1.8 - - - -
52B GLY* 4.0 5.0 - - - -
53B PRO* 3.2 33.3 - - - +
56B ARG* 2.2 74.1 + - - +
78B HIS 6.0 0.2 - - - -
79B GLY* 4.3 10.8 - - - -
80B THR* 3.1 23.2 + - - +
82B GLU* 1.3 83.7 - - - +
84B HIS* 1.3 84.8 + + - +
86B GLU* 3.2 9.1 + - - +
87B THR* 4.3 2.0 - - - -
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Residues in contact with HIS 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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51B ILE 6.0 1.3 - - - -
74B LEU* 4.1 17.9 - - + +
75B ASN 3.4 22.7 + - - -
76B PHE* 3.7 44.9 - + + -
78B HIS 2.9 28.6 + - - -
79B GLY* 3.8 5.5 - - - -
80B THR 3.0 27.3 + - - +
81B HIS* 4.1 2.5 - + - +
83B TYR* 1.3 95.7 - + - +
85B ALA* 1.3 57.6 + - - +
87B THR* 3.0 11.9 + - - -
88B ILE* 2.9 32.4 + - - +
231B PHE* 4.2 5.4 - - + -
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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 HIS 2.8 24.3 + - - +
82B GLU* 3.9 5.8 - - - +
84B HIS* 1.3 73.1 - - - +
86B GLU* 1.3 57.7 - - - +
88B ILE* 3.5 5.0 + - - +
89B LYS* 3.1 24.9 + - - +
231B PHE* 3.8 17.8 - - + -
235B GLN* 4.1 21.8 - - - +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ARG* 3.3 19.5 + - - +
82B GLU 3.4 9.5 + - - +
83B TYR* 3.2 9.3 + - - +
84B HIS 3.2 0.4 - - - -
85B ALA* 1.3 75.6 - - - +
87B THR* 1.3 61.9 + - - +
89B LYS* 3.2 13.8 + - + +
90B ASN* 2.8 50.0 + - - +
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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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51B ILE* 3.7 28.9 - - + +
52B GLY* 6.2 0.2 - - - -
56B ARG* 2.4 43.3 + - + +
61B LEU* 5.7 0.2 - - + -
74B LEU* 3.7 27.1 - - + -
83B TYR* 3.3 4.7 + - - -
84B HIS* 3.0 13.2 + - - -
86B GLU* 1.3 78.9 - - - +
88B ILE* 1.3 51.6 + - - +
90B ASN* 3.0 12.4 + - + +
91B VAL* 2.8 40.8 + - + +
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Residues in contact with ILE 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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74B LEU* 3.6 24.5 - - + -
76B PHE* 6.1 0.2 - - + -
84B HIS 2.9 19.0 + - - +
85B ALA 3.6 7.0 - - - +
87B THR* 1.3 75.7 - - - +
89B LYS* 1.3 63.0 + - - +
91B VAL* 3.4 6.9 + - - +
92B ARG* 3.0 62.0 + - + +
110B VAL* 4.2 19.5 - - + -
112B LEU* 6.3 0.2 - - + -
231B PHE* 4.8 7.2 - - + -
235B GLN* 3.7 37.9 - - + +
237B VAL* 4.3 7.2 - - + -
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Residues in contact with LYS 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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85B ALA 3.1 15.4 + - - +
86B GLU* 3.4 19.1 - - + +
88B ILE* 1.3 76.9 - - - +
90B ASN* 1.3 58.3 + - - +
92B ARG* 3.5 5.1 + - - +
93B THR* 2.5 48.7 + - - +
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Residues in contact with ASN 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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56B ARG* 3.1 44.7 + - - +
57B SER* 5.0 1.6 - - - +
58B VAL* 3.9 22.6 - - + +
61B LEU* 3.5 7.2 - - + +
86B GLU* 2.8 41.4 + - - +
87B THR* 3.0 8.7 + - - +
89B LYS* 1.3 81.5 + - - +
91B VAL* 1.3 64.6 + - - +
93B THR* 3.5 2.3 + - - -
94B ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 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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51B ILE* 4.8 1.1 - - + -
61B LEU* 3.6 22.9 - - + -
65B ILE* 4.8 1.5 - - + +
69B MET* 5.5 2.9 - - + -
72B ALA* 3.9 22.4 - - + -
74B LEU* 5.6 1.8 - - + -
87B THR* 2.8 33.4 + - + +
88B ILE* 3.4 8.7 + - - +
90B ASN* 1.3 74.2 - - - +
92B ARG* 1.3 55.6 + - + +
94B ALA* 3.4 2.6 + - - +
95B THR* 2.7 43.3 + - - +
108B VAL* 4.2 17.9 - - + +
110B VAL* 4.1 23.1 - - + -
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Residues in contact with ARG 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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88B ILE* 3.0 40.7 + - + +
89B LYS* 4.0 5.2 - - - +
91B VAL* 1.3 79.1 - - + +
93B THR* 1.3 65.9 + - - +
95B THR* 3.7 6.2 - - - -
96B GLU* 3.0 36.7 + - + +
110B VAL* 4.5 14.0 - - + +
235B GLN* 2.4 35.7 + - - -
236B ASP* 3.0 26.0 + - - +
237B VAL* 4.3 1.8 - - - +
461B ARG* 6.0 2.2 - - - +
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Residues in contact with THR 93 (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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58B VAL* 4.2 22.4 - - + -
89B LYS* 2.5 37.6 + - - +
90B ASN* 3.7 4.7 + - - -
91B VAL 3.4 0.2 - - - -
92B ARG* 1.3 79.1 - - - +
94B ALA* 1.3 60.7 - - - +
96B GLU* 3.4 4.2 + - - +
97B SER* 3.3 17.8 + - - -
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Residues in contact with ALA 94 (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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58B VAL* 3.7 30.2 - - + +
61B LEU* 3.7 16.2 - - + -
62B LYS* 3.9 10.1 - - + +
65B ILE* 4.2 5.2 - - + -
90B ASN 3.1 15.8 + - - +
91B VAL 3.7 3.8 - - - +
93B THR* 1.3 78.8 - - - +
95B THR* 1.3 59.9 + - - +
97B SER* 2.6 30.0 + - - -
98B PHE* 3.5 7.1 - - - -
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Residues in contact with THR 95 (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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65B ILE* 3.7 12.6 - - + +
91B VAL* 2.7 25.4 + - - +
92B ARG* 3.7 7.8 - - - -
93B THR 3.3 0.2 - - - -
94B ALA* 1.3 77.9 - - - +
96B GLU* 1.3 65.5 + - - +
97B SER 3.1 1.3 + - - -
98B PHE* 3.4 16.2 + - - +
105B TYR* 3.3 35.1 - - + +
106B ARG 3.7 17.6 - - - +
108B VAL* 3.6 31.0 + - + +
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Residues in contact with GLU 96 (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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92B ARG* 3.0 22.2 + - + +
93B THR* 4.0 4.9 - - - +
94B ALA 3.3 0.2 - - - -
95B THR* 1.3 83.2 - - - +
97B SER* 1.3 62.8 + - - +
98B PHE 3.0 2.7 - - - -
99B ALA* 3.1 34.0 + - + +
100B SER* 4.6 1.2 + - - -
105B TYR* 3.1 27.4 + - - -
475B LYS* 5.2 3.8 - - - -
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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