Contacts of the helix formed by residues 91 - 108 (chain B) in PDB entry 3DNJ
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 TYR 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER 4.5 1.4 + - - -
41B TYR* 3.3 55.2 - + + +
90B THR* 1.3 73.4 - - - +
92B GLU* 1.3 75.9 + - + +
94B ALA* 3.3 2.8 + - - +
95B GLU* 2.9 68.4 + - + +
116B MET* 3.5 20.5 - - + +
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Residues in contact with GLU 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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90B THR* 4.3 8.4 + - - +
91B TYR* 1.3 93.6 + - + +
93B VAL* 1.3 60.9 + - + +
95B GLU* 3.4 19.5 + - - +
96B THR* 2.8 29.6 + - - -
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Residues in contact with VAL 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 TYR* 3.7 27.8 - - + -
90B THR* 3.2 22.0 + - - +
92B GLU* 1.3 77.2 - - + +
94B ALA* 1.3 63.1 + - - +
96B THR* 3.1 10.0 + - + +
97B LYS* 2.9 34.9 + - - +
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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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41B TYR* 3.9 18.2 - - + +
43B VAL* 3.8 23.2 - - + +
89B TYR* 3.7 8.1 - - + +
90B THR 2.8 15.9 + - - +
91B TYR 3.5 4.3 - - - +
93B VAL* 1.3 75.5 - - - +
95B GLU* 1.3 63.3 + - - +
97B LYS* 3.2 2.4 + - - +
98B VAL* 3.0 27.5 + - - +
116B MET* 3.7 19.7 - - + -
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Residues in contact with GLU 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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91B TYR* 2.9 49.3 + - + +
92B GLU* 3.6 20.2 - - - +
93B VAL 3.2 0.2 - - - -
94B ALA* 1.3 77.2 - - - +
96B THR* 1.3 62.3 + - - +
98B VAL* 3.5 4.3 + - - +
99B ALA* 3.0 25.1 + - - +
116B MET* 3.6 19.5 - - - -
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Residues in contact with THR 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 GLU 2.8 19.6 + - - -
93B VAL* 3.1 14.5 + - + +
95B GLU* 1.3 76.9 - - - +
97B LYS* 1.3 58.9 + - + +
99B ALA* 3.3 6.0 + - - +
100B GLN* 2.9 58.5 + - + +
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Residues in contact with LYS 97 (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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43B VAL* 4.3 4.0 - - + -
63B PHE* 2.8 34.5 + - + +
64B PHE* 3.8 17.9 - - + -
89B TYR* 3.9 38.3 + - + -
93B VAL* 2.9 27.0 + - - +
94B ALA 3.6 6.1 - - - +
96B THR* 1.3 75.5 - - + +
98B VAL* 1.3 66.1 + - - +
100B GLN* 3.2 18.8 + - - +
101B VAL* 2.9 29.0 + - - +
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Residues in contact with VAL 98 (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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43B VAL* 4.0 10.3 - - + -
94B ALA 3.0 19.2 + - - +
95B GLU* 3.7 7.2 - - - +
97B LYS* 1.3 76.5 - - - +
99B ALA* 1.3 64.4 + - - +
101B VAL* 3.3 2.6 + - - +
102B ILE* 3.0 34.0 + - + +
114B CYS* 3.5 31.8 - - - +
115B THR* 3.6 30.1 - - - +
116B MET* 4.1 15.3 - - + -
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Residues in contact with ALA 99 (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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95B GLU 3.0 17.9 + - - +
96B THR* 3.6 6.1 - - - +
98B VAL* 1.3 78.7 - - - +
100B GLN* 1.3 59.1 + - + +
102B ILE* 3.3 7.7 + - - +
103B ASP* 2.9 32.3 + - - +
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Residues in contact with GLN 100 (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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63B PHE* 3.6 33.8 - - + -
96B THR* 2.9 41.9 + - + +
97B LYS* 3.2 18.6 + - - +
99B ALA* 1.3 75.5 - - + +
101B VAL* 1.3 59.1 + - - +
103B ASP* 3.8 7.8 - - - +
104B SER* 3.0 30.7 + - - -
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Residues in contact with VAL 101 (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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45B ILE* 4.7 2.2 - - + -
55B PHE* 5.4 0.3 - - - -
59B VAL* 3.9 16.4 - - + -
63B PHE* 4.4 9.4 - - + -
64B PHE* 3.5 34.1 - - + -
97B LYS 2.9 20.8 + - - +
98B VAL 3.6 4.0 - - - +
100B GLN* 1.3 74.6 - - - +
102B ILE* 1.3 61.0 + - - +
104B SER* 3.4 4.7 + - - -
105B ALA* 2.8 29.4 + - + +
112B LEU* 3.9 26.2 - - + +
114B CYS* 3.8 24.9 - - + -
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Residues in contact with ILE 102 (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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98B VAL* 3.0 39.6 + - + +
99B ALA* 3.9 6.1 - - - +
101B VAL* 1.3 76.1 - - - +
103B ASP* 1.3 66.4 + - - +
105B ALA* 3.3 4.0 + - - -
106B ARG* 2.9 54.4 + - + +
112B LEU 4.7 1.6 - - - +
113B GLN* 5.5 0.2 - - - -
114B CYS* 3.9 24.2 - - + +
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Residues in contact with ASP 103 (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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99B ALA 2.9 17.3 + - - +
100B GLN* 3.8 8.1 - - - +
102B ILE* 1.3 79.5 - - - +
104B SER* 1.3 61.2 + - - +
106B ARG* 4.0 2.9 - - - +
107B ARG* 2.9 66.5 + - - +
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Residues in contact with SER 104 (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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55B PHE* 3.6 11.2 - - - -
58B TYR* 4.3 3.5 + - - -
59B VAL* 5.3 0.7 - - - -
62B ARG* 5.5 0.2 - - - -
63B PHE* 3.8 27.4 - - - -
100B GLN 3.0 19.0 + - - -
101B VAL* 3.7 3.1 - - - -
103B ASP* 1.3 75.7 - - - +
105B ALA* 1.3 64.3 + - - +
107B ARG* 3.3 17.6 + - - +
108B HIS* 2.7 47.6 + - - -
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Residues in contact with ALA 105 (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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55B PHE* 3.7 18.3 - - + -
101B VAL 2.8 22.1 + - - +
102B ILE 3.3 0.9 + - - +
104B SER* 1.3 74.6 + - - +
106B ARG* 1.3 81.9 + - - +
108B HIS* 3.1 10.0 + - - +
109B GLN 3.1 0.2 + - - -
110B HIS* 2.9 28.6 + - - +
112B LEU* 3.8 22.9 - - + +
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Residues in contact with ARG 106 (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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102B ILE* 2.9 43.4 + - + +
103B ASP* 4.2 3.1 - - - +
105B ALA* 1.3 85.0 - - - +
107B ARG* 1.3 60.1 + - + +
109B GLN* 2.9 26.4 + - - +
110B HIS 2.9 25.6 + - - +
111B PRO* 3.2 17.6 + - - +
112B LEU 2.8 30.3 + - - +
113B GLN* 4.7 4.2 - - - +
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Residues in contact with ARG 107 (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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63B PHE* 6.0 1.2 - - - -
103B ASP* 2.9 52.1 + - - +
104B SER* 3.8 18.4 - - - +
106B ARG* 1.3 75.6 - - + +
108B HIS* 1.3 69.5 + - - +
109B GLN* 3.3 9.5 + - - +
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Residues in contact with HIS 108 (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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55B PHE* 3.4 20.9 - + + -
58B TYR* 4.0 20.8 + + - -
104B SER* 2.7 46.6 + - - +
105B ALA 3.1 4.0 + - - +
107B ARG* 1.3 88.1 - - - +
109B GLN* 1.3 72.2 + - - +
110B HIS* 3.2 32.0 + - + +
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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