Contacts of the helix formed by residues 84 - 97 (chain B) in PDB entry 1J7H
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 ASP 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.3 47.0 - - + +
81B ASP* 2.7 32.2 + - + +
83B ASN* 1.3 78.4 - - - +
85B PHE* 1.3 60.1 + - - +
86B ALA 2.9 7.6 + - - -
87B ALA* 2.9 20.4 + - - +
88B VAL* 3.3 13.1 + - + +
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Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 5.2 2.9 - - + -
79B VAL* 3.6 27.8 - - + +
81B ASP 3.5 3.0 + - - +
82B LEU* 3.3 30.2 + - + +
83B ASN 3.3 0.4 - - - -
84B ASP* 1.3 78.5 - - - +
86B ALA* 1.3 54.4 + - - +
87B ALA 3.1 0.2 - - - -
88B VAL* 3.6 17.9 - - + -
89B ASN* 2.6 66.1 + - + +
107B ARG* 3.1 31.6 - - - -
109B CYS* 3.8 27.1 - - + -
116C PRO* 6.3 3.6 - - + -
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU 4.4 1.0 + - - -
83B ASN 3.8 15.7 + - - +
84B ASP 2.9 0.8 + - - -
85B PHE* 1.3 79.2 - - - +
87B ALA* 1.3 55.8 + - - +
89B ASN* 4.6 2.8 - - - +
90B ALA* 3.3 23.7 + - - +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 5.4 1.8 - - + -
48B VAL* 4.5 24.6 - - + +
84B ASP* 2.9 14.4 + - - +
86B ALA* 1.3 77.3 - - - +
88B VAL* 1.3 67.2 + - + +
89B ASN 3.4 0.4 - - - -
90B ALA* 3.6 5.0 + - - +
91B GLU* 3.1 24.4 + - - +
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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
----------------------------------------------------------
47B ILE* 3.8 22.4 - - + -
48B VAL* 5.9 0.9 - - - +
51B ALA* 4.1 26.2 - - + +
55B LEU* 6.2 2.5 - - + -
77B VAL* 5.9 6.7 - - + -
79B VAL* 5.8 4.9 - - + -
84B ASP* 3.5 17.5 - - + +
85B PHE* 3.2 21.5 + - + +
87B ALA* 1.3 76.4 - - + +
89B ASN* 1.3 54.9 + - - +
91B GLU* 3.6 3.2 - - - +
92B TYR* 2.6 47.5 + - + +
107B ARG* 5.6 1.1 - - - +
121B LEU* 5.7 4.3 - - + -
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Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 2.6 54.4 + - + +
86B ALA* 4.6 3.1 - - - +
88B VAL* 1.3 71.1 - - - +
90B ALA* 1.3 66.1 + - - +
92B TYR* 3.8 5.9 - - - +
93B GLU* 3.1 23.6 + - - +
107B ARG* 3.8 7.5 + - - +
16C GLY* 5.4 2.0 - - - -
17C PRO* 3.9 23.7 - - - +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA 3.3 20.5 + - - +
87B ALA* 3.9 6.1 - - - +
88B VAL 3.3 0.6 - - - -
89B ASN* 1.3 81.2 - - - +
91B GLU* 1.3 57.9 + - - +
93B GLU* 4.7 2.6 - - - +
94B ARG* 3.1 26.5 + - - +
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 5.1 16.4 - - + +
51B ALA* 5.4 2.6 - - - +
52B ARG* 3.7 31.7 + - - +
55B LEU* 4.5 10.7 - - - +
87B ALA 3.1 18.4 + - - +
88B VAL* 4.1 3.4 - - - +
90B ALA* 1.3 77.4 - - - +
92B TYR* 1.3 64.4 + - - +
93B GLU 3.4 0.4 - - - -
94B ARG* 3.8 6.9 - - + +
95B PHE* 3.1 31.8 + - - +
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Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.8 24.7 - - + -
75B THR* 3.1 34.0 + - + +
77B VAL* 5.2 3.6 - - + -
88B VAL* 2.6 32.5 + - + +
89B ASN* 3.4 5.4 + - - +
91B GLU* 1.3 75.6 - - - +
93B GLU* 1.3 58.3 + - - +
95B PHE* 2.9 34.4 - + - -
96B PHE* 3.1 46.4 + + - -
105B PRO* 5.1 1.2 + - - +
107B ARG* 3.1 43.6 - - - +
123B ILE* 6.2 0.9 - - + -
17C PRO* 3.3 35.4 + - + -
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Residues in contact with GLU 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 ASN* 3.1 16.9 + - - +
90B ALA* 4.7 2.2 - - - +
92B TYR* 1.3 74.2 - - - +
94B ARG* 1.3 74.6 + - - +
95B PHE 3.2 2.6 + - - -
96B PHE* 3.5 3.0 + - - +
97B LYS* 3.5 26.7 + - - +
104B PHE* 3.6 20.1 - - + -
15C ILE 5.7 0.7 - - - -
16C GLY* 3.4 11.0 - - - +
17C PRO* 3.4 42.6 - - + -
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Residues in contact with ARG 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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90B ALA 3.1 21.6 + - - +
91B GLU* 3.9 9.4 - - + +
92B TYR 3.4 0.6 - - - -
93B GLU* 1.3 87.9 + - - +
95B PHE* 1.3 57.8 + - - +
97B LYS* 5.0 2.1 - - - +
98B GLU* 2.8 54.6 + - - +
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 5.5 11.0 - - - +
55B LEU* 3.3 49.6 - - + -
59B LYS* 5.8 4.3 - - + -
69B ALA* 4.5 7.0 - - + -
72B ILE* 6.0 0.2 - - + -
91B GLU* 3.1 23.6 + - - +
92B TYR* 2.9 20.6 - + - -
93B GLU 3.2 0.2 - - - -
94B ARG* 1.3 78.7 - - - +
96B PHE* 1.3 92.2 + + - +
98B GLU* 3.1 5.8 + - - -
99B ASN* 2.6 55.5 + - - +
101B HIS* 3.8 19.7 - + - -
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.7 1.1 - - + -
69B ALA 4.1 7.2 - - - -
72B ILE* 4.1 15.5 - - + -
75B THR* 5.6 0.2 - - + -
92B TYR* 3.1 44.6 + + - +
93B GLU* 3.5 10.5 + - - +
95B PHE* 1.3 127.2 - + - +
97B LYS* 1.3 54.5 + - - +
99B ASN 2.8 2.9 + - - -
100B ASN 2.8 10.6 + - - -
101B HIS* 2.5 69.9 + - + +
104B PHE* 5.1 6.1 - + + -
105B PRO* 3.3 35.9 - - + -
17C PRO* 5.2 3.6 - - + -
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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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93B GLU* 3.5 22.1 + - - +
94B ARG* 5.0 2.0 - - - +
96B PHE* 1.3 80.3 - - - +
98B GLU* 1.3 61.5 + - + +
99B ASN 3.1 0.7 + - - -
100B ASN* 3.3 9.5 + - - -
101B HIS 4.1 8.0 + - - +
102B PRO* 4.1 26.5 - - + -
104B PHE* 5.6 3.1 - - + -
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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