Contacts of the helix formed by residues 85 - 97 (chain R) in PDB entry 3SN6
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 ALA 85 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81R VAL* 3.3 6.0 + - + +
84R LEU* 1.3 81.0 - - + +
86R VAL* 1.3 69.0 + - - +
87R VAL 3.5 0.2 - - - -
88R PRO* 3.6 0.3 - - - +
89R PHE* 3.2 43.3 + - + +
108R PHE* 5.6 3.1 - - + -
109R TRP* 4.4 2.5 - - + -
112R ILE* 3.6 34.1 - - + -
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Residues in contact with VAL 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R VAL 3.6 9.8 + - - +
82R MET* 3.4 12.6 + - - +
85R ALA* 1.3 74.9 - - - +
87R VAL* 1.3 58.6 + - - +
90R GLY* 2.9 26.5 + - - -
109R TRP* 3.2 18.6 + - + +
112R ILE* 3.4 31.6 - - + +
113R ASP* 3.5 28.5 - - + +
116R CYS* 4.5 8.3 - - + -
316R TYR* 3.4 36.9 - - + +
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Residues in contact with VAL 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R ILE* 4.2 11.0 - - + -
44R VAL* 3.5 23.6 - - + -
47R ILE* 3.7 15.7 - - + -
82R MET* 2.7 39.8 + - + +
83R GLY* 3.7 3.6 - - - -
86R VAL* 1.3 70.6 - - - +
88R PRO* 1.3 64.4 - - + +
90R GLY* 3.3 0.9 + - - -
91R ALA* 2.9 26.7 + - - +
313R TRP* 3.5 24.1 - - + -
316R TYR* 3.9 25.6 - - + -
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Residues in contact with PRO 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R VAL* 4.0 23.8 - - + -
83R GLY 3.2 22.7 - - - +
84R LEU* 2.9 29.4 - - - +
85R ALA 3.6 2.0 - - - +
87R VAL* 1.3 95.2 - - + +
89R PHE* 1.3 63.7 + - + +
91R ALA* 3.1 4.8 + - + +
92R ALA* 2.9 29.1 + - - +
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Residues in contact with PHE 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R LEU 5.2 3.4 - - - -
85R ALA* 3.2 29.4 + - + +
88R PRO* 1.3 85.9 - - + +
90R GLY* 1.3 57.2 + - - +
92R ALA* 3.6 8.8 + - + +
93R HIS* 2.9 27.7 + - - +
101R PHE* 5.9 4.7 - - + -
105R TRP* 3.6 33.0 - + - -
108R PHE* 6.3 0.9 - + - -
109R TRP* 3.3 30.3 - + + +
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Residues in contact with GLY 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R VAL 2.9 17.6 + - - -
87R VAL* 3.7 2.0 - - - -
88R PRO 3.2 0.2 - - - -
89R PHE* 1.3 75.5 - - - +
91R ALA* 1.3 59.2 - - - +
93R HIS* 3.1 10.6 + - - +
94R ILE* 2.9 31.9 + - - +
109R TRP* 3.9 14.9 - - - +
313R TRP* 3.7 12.3 - - - -
316R TYR* 5.9 2.7 - - - -
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Residues in contact with ALA 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R MET* 3.7 24.4 - - + +
44R VAL* 4.7 4.7 - - + -
87R VAL 2.9 14.9 + - - +
88R PRO* 3.4 11.7 - - + +
90R GLY* 1.3 72.6 - - - +
92R ALA* 1.3 65.9 + - - +
94R ILE* 2.9 6.3 + - - +
95R LEU* 2.9 29.6 + - + +
313R TRP* 3.4 20.8 - - + -
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Residues in contact with ALA 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88R PRO 2.9 15.6 + - - +
89R PHE* 3.8 9.4 - - + +
91R ALA* 1.3 76.0 - - - +
93R HIS* 1.3 57.5 + - - +
95R LEU* 3.1 14.0 + - + +
96R THR* 2.9 39.0 + - - +
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Residues in contact with HIS 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89R PHE 2.9 16.4 + - - +
90R GLY* 3.1 17.1 + - - +
92R ALA* 1.3 77.9 - - - +
94R ILE* 1.3 64.5 + - - +
97R LYS* 3.3 18.1 + - - -
98R THR* 3.7 17.1 + - - -
99R TRP* 4.0 31.9 + - + +
109R TRP* 5.4 12.4 - + + -
191R CYS* 3.3 26.9 + - + -
309R ILE* 5.9 7.9 - - + +
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Residues in contact with ILE 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R MET* 5.6 7.0 - - + -
40R MET* 3.6 26.7 - - + -
90R GLY 2.9 10.9 + - - +
91R ALA 2.9 5.3 + - - +
93R HIS* 1.3 82.6 - - - +
95R LEU* 1.3 63.0 + - - +
96R THR 3.5 0.2 - - - -
97R LYS* 3.9 7.9 + - - +
309R ILE* 4.2 18.4 - - + -
313R TRP* 3.2 42.2 - - + +
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Residues in contact with LEU 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33R VAL* 4.0 37.3 - - + +
36R MET* 5.1 2.0 - - + -
37R GLY* 4.2 12.6 - - - +
40R MET* 4.1 20.4 - - + -
91R ALA* 2.9 21.9 + - + +
92R ALA* 3.1 16.1 + - + +
94R ILE* 1.3 82.0 - - - +
96R THR* 1.3 62.4 + - - +
97R LYS* 3.6 1.9 + - - +
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Residues in contact with THR 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92R ALA* 2.9 19.1 + - - +
95R LEU* 1.3 75.9 - - - +
97R LYS* 1.3 69.1 + - - +
98R THR* 3.2 20.1 + - - +
100R THR* 3.9 21.5 + - - +
1157R THR* 6.0 1.7 - - - +
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Residues in contact with LYS 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93R HIS* 3.3 11.3 + - - -
94R ILE* 3.9 7.3 + - - +
95R LEU 3.3 4.1 - - - +
96R THR* 1.3 79.9 - - - +
98R THR* 1.3 62.2 + - - +
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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