Contacts of the helix formed by residues 82 - 94 (chain R) in PDB entry 3J7Y
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 LYS 82 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2243A A 4.1 4.0 + - - -
2244A U 3.2 36.2 + - - +
73R THR* 6.1 0.2 - - - -
76R SER* 3.8 2.9 - - - -
77R GLN* 4.5 20.0 - - - +
81R LEU* 1.3 81.2 - - - +
83R TYR* 1.3 68.8 + - - +
84R PRO* 3.3 12.8 - - + -
85R ALA* 3.5 9.5 + - + +
86R LEU* 3.1 21.5 + - - +
124R ARG* 5.3 5.5 - - - +
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Residues in contact with TYR 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2247A C 3.4 33.4 - - - -
2248A U 2.7 28.4 + - - -
69R ILE* 3.6 24.7 - - + +
72R ILE* 3.6 28.0 - - + -
73R THR* 3.4 31.0 - - + +
76R SER* 3.6 9.4 + - - -
82R LYS* 1.3 72.2 - - - +
84R PRO* 1.3 69.2 - - + +
86R LEU* 3.2 6.9 + - - +
87R ILE* 3.0 47.7 + - + +
99R ARG* 2.9 29.2 + - - -
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Residues in contact with PRO 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2246A A 4.4 18.2 - - + +
2247A C 3.3 56.7 + - - +
82R LYS* 3.3 15.3 - - + -
83R TYR* 1.3 94.9 - - + +
85R ALA* 1.3 65.8 + - - +
87R ILE* 3.3 2.6 + - + +
88R GLY* 2.9 20.1 + - - -
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Residues in contact with ALA 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2246A A 5.1 4.3 - - - -
81R LEU* 4.2 5.6 - - + -
82R LYS* 3.7 13.2 - - + +
84R PRO* 1.3 81.3 - - - +
86R LEU* 1.3 59.0 + - - +
88R GLY* 3.2 0.6 + - - -
89R ASN* 2.7 41.7 + - - +
124R ARG* 3.2 42.2 - - - +
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Residues in contact with LEU 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R ILE* 3.7 30.5 - - + -
76R SER* 4.0 13.5 - - - -
81R LEU* 4.6 10.3 - - + +
82R LYS 3.1 10.7 + - - +
83R TYR 3.2 8.5 + - - +
85R ALA* 1.3 80.7 - - - +
87R ILE* 1.3 60.2 - - + +
89R ASN* 3.2 8.1 + - - +
90R LEU* 2.9 47.3 + - + +
102R LEU* 4.9 4.9 - - + -
113R PHE* 3.9 20.0 - - + -
116R LEU* 4.5 3.6 - - + +
117R ALA* 4.4 15.7 - - - +
120R ALA* 3.8 19.1 - - + -
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Residues in contact with ILE 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2247A C 5.0 3.6 - - - +
2248A U 4.9 1.3 - - - +
72R ILE* 5.0 2.5 - - + -
83R TYR* 3.0 51.0 + - + +
84R PRO* 3.8 4.9 - - + +
86R LEU* 1.3 78.4 - - + +
88R GLY* 1.3 69.2 + - - +
90R LEU* 3.2 8.5 + - + +
91R VAL* 2.9 30.6 + - + +
97R LEU 5.9 0.2 - - - +
99R ARG* 3.4 43.1 - - - +
102R LEU* 4.3 18.4 - - + -
24j GLY 4.3 14.6 - - - +
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Residues in contact with GLY 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2247A C 3.4 22.2 + - - -
84R PRO 2.9 11.0 + - - -
85R ALA 3.7 2.2 - - - -
87R ILE* 1.3 78.9 - - - +
89R ASN* 1.3 61.3 + - - +
91R VAL* 3.2 8.7 + - - +
92R LYS* 2.9 41.0 + - - +
24j GLY 4.9 2.5 - - - -
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Residues in contact with ASN 89 (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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81R LEU* 4.9 2.1 - - - +
85R ALA* 2.7 30.2 + - - +
88R GLY* 1.3 80.6 - - - +
90R LEU* 1.3 56.4 + - - +
92R LYS* 3.2 25.0 + - - +
93R CYS* 2.9 33.6 + - - -
120R ALA* 3.0 45.9 - - + +
121R SER* 4.9 0.2 - - - -
123R ARG* 3.8 8.3 - - + +
124R ARG* 3.5 29.2 - - - +
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Residues in contact with LEU 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R LEU* 2.9 39.5 + - + +
87R ILE* 3.6 10.3 - - + +
89R ASN* 1.3 76.0 - - - +
91R VAL* 1.3 64.6 + - + +
93R CYS* 3.2 5.3 + - - +
94R GLN 3.1 4.0 + - - -
95R VAL* 3.0 63.4 + - + +
97R LEU* 5.7 2.0 - - + +
102R LEU* 4.0 33.9 - - + -
116R LEU* 4.0 30.7 - - + +
119R LEU* 4.8 5.8 - - + -
120R ALA* 5.0 2.5 - - + +
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Residues in contact with VAL 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2149A G 5.5 2.0 - - - +
87R ILE* 2.9 27.3 + - + +
88R GLY* 3.5 8.1 - - - +
90R LEU* 1.3 76.8 - - + +
92R LYS* 1.3 63.8 + - + +
94R GLN* 3.1 13.1 + - - +
95R VAL 4.6 4.0 - - - +
96R GLU* 5.1 4.5 - - + +
24j GLY* 3.8 27.8 - - - +
25j GLY* 4.0 7.2 - - - -
27j TRP* 3.4 26.0 - - + -
28j ARG* 3.5 37.7 + - - +
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Residues in contact with LYS 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2246A A 5.3 7.3 + - - -
2247A C 6.0 0.4 - - - -
88R GLY* 2.9 25.7 + - - +
89R ASN* 3.2 22.3 + - - +
91R VAL* 1.3 76.8 - - + +
93R CYS* 1.3 61.0 + - - +
94R GLN* 3.2 2.9 + - - +
123R ARG* 3.3 47.4 + - - +
124R ARG* 6.1 1.0 - - - +
143R SER* 6.2 0.5 - - - -
144R ARG 4.7 3.5 - - - +
145R VAL* 4.3 3.5 - - - +
27j TRP* 3.3 63.1 - - + -
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Residues in contact with CYS 93 (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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89R ASN 2.9 11.8 + - - +
90R LEU* 3.2 11.9 + - - +
92R LYS* 1.3 75.1 - - - +
94R GLN* 1.3 70.4 + - - +
95R VAL* 4.0 16.4 - - + +
119R LEU* 3.5 33.7 - - + -
120R ALA 5.6 0.2 - - - -
123R ARG* 3.3 31.6 - - - -
142R PHE* 4.4 13.0 - - - -
144R ARG 5.3 2.0 - - - +
146S LYS* 3.6 25.7 + - - +
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Residues in contact with GLN 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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90R LEU 3.1 2.8 + - - -
91R VAL 3.1 8.0 + - - +
92R LYS 3.1 11.1 - - - +
93R CYS* 1.3 81.8 - - - +
95R VAL* 1.3 61.6 + - - +
96R GLU* 3.7 11.7 - - + +
144R ARG 5.2 0.7 - - - +
145R VAL* 3.3 32.6 - - + +
146R VAL* 3.3 38.3 + - - +
148R TYR* 5.3 2.6 - - - -
146S LYS* 3.7 25.3 - - + +
147S PRO* 3.2 32.0 - - + +
27j TRP* 4.3 7.2 - - + -
33j LEU* 3.9 20.8 - - + +
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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
------------------------------------------------------------
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