Contacts of the helix formed by residues 84 - 94 (chain B) in PDB entry 3N9Y
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 ILE 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 4.4 3.8 - - + -
83B LEU* 1.3 69.9 - - - +
85B PRO* 1.3 68.1 - - - +
86B PRO* 3.6 16.4 - - + -
87B TRP* 3.0 70.4 + - + +
88B VAL* 3.1 12.2 + - - +
102B LEU* 5.7 1.6 - - - +
209B LEU* 4.0 18.4 - - + -
460B LEU* 4.0 19.5 - - + -
602B CLR 3.9 44.2 - - + -
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Residues in contact with PRO 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASN* 5.8 2.7 - - - +
82B PHE* 3.9 19.3 - - + -
83B LEU 3.2 10.1 - - - +
84B ILE* 1.3 84.8 - - + +
86B PRO* 1.3 71.3 - - + +
88B VAL* 3.4 8.0 + - + +
89B ALA* 2.9 24.4 + - - +
209B LEU* 3.9 18.6 - - + +
211B LEU 4.2 9.4 - - - +
213B PRO* 4.8 10.3 - - + +
216B PHE* 4.0 15.8 - - + -
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Residues in contact with PRO 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 3.6 16.6 - - + -
85B PRO* 1.3 99.8 - - + +
87B TRP* 1.3 60.8 + - + +
90B TYR* 3.0 29.8 + - - +
205B SER* 4.2 11.9 - - - +
208B MET* 3.6 49.8 - - + +
209B LEU* 5.0 1.3 - - + -
216B PHE* 3.7 17.9 - - + -
224B TRP* 3.5 6.8 - - + -
227B HIS* 3.8 9.8 + - + +
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Residues in contact with TRP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 3.0 39.5 + - + +
86B PRO* 1.3 72.7 - - + +
88B VAL* 1.3 65.4 + - - +
90B TYR* 3.4 1.4 + - - +
91B HIS* 2.7 35.9 + - + +
101B LEU* 3.7 32.1 - - + -
102B LEU* 4.7 12.8 - - + -
201B MET* 3.3 14.6 - - - -
202B PHE* 3.7 23.6 - + - -
205B SER* 2.9 20.9 + - - -
227B HIS* 3.6 16.2 - - - -
231B TRP* 3.8 24.5 - + + +
460B LEU* 3.4 33.7 - - + -
602B CLR 4.1 26.2 - - + -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.8 32.1 - - + -
84B ILE 3.1 12.3 + - - +
85B PRO* 3.7 9.9 - - + +
87B TRP* 1.3 75.8 - - - +
89B ALA* 1.3 58.0 + - - +
91B HIS* 3.2 6.1 + - - +
92B GLN* 2.9 60.0 + - + +
102B LEU* 4.4 18.2 - - + -
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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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85B PRO 2.9 18.3 + - - +
86B PRO 3.8 1.1 - - - +
88B VAL* 1.3 77.1 - - - +
90B TYR* 1.3 55.3 + - - +
92B GLN* 4.7 5.2 - - - -
93B TYR* 2.8 38.2 + - - +
213B PRO* 4.4 8.3 - - + -
216B PHE* 4.0 13.9 - - + -
217B ARG* 3.9 15.5 - - - +
224B TRP* 3.8 19.1 - - + -
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Residues in contact with TYR 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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86B PRO 3.0 17.4 + - - +
87B TRP 3.7 3.4 - - - +
88B VAL 3.3 0.2 - - - -
89B ALA* 1.3 76.8 - - - +
91B HIS* 1.3 69.6 + - - +
94B TYR* 3.0 54.5 + + + +
96B ARG* 3.2 35.8 + - + -
224B TRP* 3.6 13.6 - - + -
227B HIS* 5.0 0.2 - - + -
228B VAL* 3.7 23.3 - - + -
231B TRP* 3.3 45.4 + + + -
232B ASP* 2.6 37.9 + - - -
235B PHE* 4.0 10.5 - + - -
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Residues in contact with HIS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 2.7 27.0 + - + +
88B VAL* 3.2 4.0 + - - +
90B TYR* 1.3 88.2 - + - +
92B GLN* 1.3 60.7 + - + +
95B GLN* 3.0 9.2 + - - -
96B ARG* 2.9 48.0 + - + +
97B PRO 4.0 3.1 + - - -
98B ILE* 3.7 32.1 - - + -
102B LEU* 3.4 22.8 - - + +
231B TRP* 3.9 33.5 - + - -
235B PHE* 3.6 20.0 - + - -
283B GLU* 5.0 7.5 + - - +
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Residues in contact with GLN 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 VAL* 2.9 40.7 + - + +
89B ALA* 4.0 4.4 - - - +
91B HIS* 1.3 76.3 - - + +
93B TYR* 1.3 66.0 + - - +
95B GLN* 3.2 20.1 + - - +
98B ILE* 6.3 1.3 - - + -
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Residues in contact with TYR 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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89B ALA 2.8 22.2 + - - +
92B GLN* 1.3 75.0 - - - +
94B TYR* 1.3 101.7 + + + +
95B GLN* 3.5 6.8 + - - +
217B ARG* 4.1 26.2 - - - +
224B TRP* 5.3 2.9 - + + -
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Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.0 39.3 + + + +
91B HIS 3.9 0.2 - - - -
93B TYR* 1.3 108.0 - + + +
95B GLN* 1.3 69.2 + - - +
96B ARG* 3.3 24.6 + - + +
224B TRP* 4.3 12.4 + + - -
228B VAL* 3.8 40.1 - - + +
232B ASP* 5.3 5.4 - - - +
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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