Contacts of the helix formed by residues 77 - 87 (chain B) in PDB entry 1NYR
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 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B LEU* 2.6 25.1 + - - +
74B ARG 2.5 13.8 + - - -
76B SER* 1.3 72.5 + - - +
78B ALA* 1.3 53.5 + - - -
79B HIS 3.0 1.3 - - - -
80B LEU* 2.9 9.3 + - + +
81B MET* 2.7 34.7 + - - +
104B PHE* 3.4 33.0 - - + -
126B MET* 4.2 3.6 - - + -
192B ILE* 4.7 8.6 - - + +
195B PHE* 3.5 32.5 - - + -
221B ALA* 3.5 10.9 - - - +
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Residues in contact with ALA 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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74B ARG 3.3 5.9 + - - +
75B HIS* 4.8 12.6 - - + +
77B THR* 1.3 77.7 - - - +
79B HIS* 1.3 58.6 + - - +
81B MET* 3.2 1.8 + - - +
82B ALA* 2.9 32.2 + - - +
97B GLY 3.9 16.6 - - - +
104B PHE* 3.6 23.6 - - + -
105B TYR 3.8 18.8 - - - +
106B TYR* 3.3 14.0 - - + -
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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
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75B HIS 4.3 2.0 - - - +
76B SER* 4.0 21.3 - - - +
77B THR 3.9 0.2 - - - +
78B ALA* 1.3 81.1 - - - +
80B LEU* 1.3 56.8 + - - +
82B ALA* 3.5 15.5 - - - +
83B HIS* 3.6 6.1 + - - +
106B TYR* 4.6 3.5 - - - -
136B ILE* 4.2 9.2 - - + -
172B TYR* 4.7 0.2 - - + -
173B SER* 3.2 33.2 + - - -
174B GLN* 2.7 42.0 + - + +
177B PHE* 4.0 23.8 - + - -
179B ASP* 4.1 17.2 + - + +
181B CYS* 4.4 3.4 - - - -
185B HIS* 3.2 36.4 + + + -
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Residues in contact with LEU 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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76B SER 3.9 2.6 + - - +
77B THR* 2.9 10.5 + - + +
79B HIS* 1.3 79.7 - - - +
81B MET* 1.3 62.8 + - - +
82B ALA 3.3 0.2 - - - -
83B HIS* 3.9 0.5 + - - +
84B ALA* 3.1 21.4 + - - +
126B MET* 3.2 26.2 - - + +
129B ILE* 3.2 48.7 - - + -
130B VAL* 4.0 7.9 - - + -
174B GLN* 4.5 4.7 - - - +
189B THR* 5.3 1.3 - - - -
192B ILE* 3.4 37.9 - - + -
195B PHE* 3.9 19.1 - - + -
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Residues in contact with MET 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 THR 2.7 18.2 + - - +
78B ALA* 3.7 1.6 - - - +
80B LEU* 1.3 71.1 - - - +
82B ALA* 1.3 69.2 + - - +
84B ALA* 2.8 18.9 + - - +
85B ILE* 3.3 14.2 + - + +
104B PHE* 3.4 14.4 - - + -
105B TYR 3.2 29.8 - - - +
106B TYR* 3.6 13.2 - - + -
108B PHE* 4.5 7.9 - - + -
122B ILE* 5.0 7.0 - - + -
126B MET* 3.4 19.0 - - + +
197B LEU* 3.2 36.3 - - + -
217B ILE* 3.2 32.3 - - + +
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Residues in contact with ALA 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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78B ALA 2.9 9.4 + - - +
79B HIS 3.5 5.4 - - - +
81B MET* 1.3 80.5 - - - +
83B HIS* 1.3 58.4 + - - +
85B ILE* 2.9 23.6 + - - +
86B LYS 3.8 1.9 + - - -
94B PHE* 4.2 4.3 - - + -
106B TYR* 2.9 39.4 - - + -
108B PHE* 4.0 10.5 - - + -
177B PHE* 3.1 26.9 - - + -
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Residues in contact with HIS 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 3.6 6.1 + - - +
80B LEU 4.6 1.8 - - - +
81B MET 3.4 0.2 - - - -
82B ALA* 1.3 74.0 - - - +
84B ALA* 1.3 57.9 + - - +
85B ILE 2.7 11.6 + - - -
86B LYS* 3.6 14.5 + - + +
87B ARG* 3.7 27.0 + - + +
129B ILE* 5.0 3.8 - - + +
134B MET* 4.8 6.4 - - + +
174B GLN* 3.4 24.7 + - - +
176B ASP* 3.2 42.7 + - + +
177B PHE* 3.2 44.2 - + + +
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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 LEU* 3.1 17.1 + - - +
81B MET* 2.8 17.3 + - - +
83B HIS* 1.3 75.9 - - - +
85B ILE* 1.3 60.2 + - - +
87B ARG* 4.8 2.2 + - - +
88B LEU 5.3 1.0 + - - -
122B ILE* 3.9 16.4 - - + +
125B THR* 3.2 27.0 - - + +
126B MET* 3.3 30.7 - - + +
129B ILE* 5.9 1.1 - - - -
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Residues in contact with ILE 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 MET* 3.6 15.0 - - + +
82B ALA 2.9 6.7 + - - +
83B HIS 2.7 2.4 - - - -
84B ALA* 1.3 80.6 - - - +
86B LYS* 1.3 55.6 + - - +
87B ARG 2.9 9.9 + - - -
88B LEU 3.9 1.2 + - - -
89B TYR* 2.7 50.0 + - + +
92B VAL* 3.3 23.1 - - + +
94B PHE* 5.4 0.7 - - + -
108B PHE* 3.5 43.5 - - + -
110B ILE* 3.9 10.5 - - + -
114B ILE* 5.2 9.0 - - + -
122B ILE* 4.9 13.9 - - + -
217B ILE* 5.3 4.9 - - + -
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Residues in contact with LYS 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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82B ALA 3.8 2.8 + - - -
83B HIS* 3.6 14.8 + - + -
85B ILE* 1.3 76.9 - - - +
87B ARG* 1.3 61.7 + - - +
89B TYR* 4.3 2.0 - - - -
90B GLY* 4.6 3.6 + - - -
91B ASN* 3.9 29.5 + - - +
92B VAL* 3.3 27.4 - - + +
93B LYS* 4.8 14.8 - - - +
94B PHE* 3.5 34.0 - - + -
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Residues in contact with ARG 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 HIS* 3.7 23.8 + - + +
84B ALA 4.9 3.8 - - - +
85B ILE 2.9 4.8 + - - +
86B LYS* 1.3 81.2 - - - +
88B LEU* 1.3 66.0 + - + +
89B TYR 3.3 2.9 + - - -
90B GLY* 4.3 4.3 + - - -
125B THR* 5.1 7.0 - - + -
128B GLN* 4.7 17.5 - - - +
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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