Contacts of the helix formed by residues 80 - 91 (chain B) in PDB entry 3N6J
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 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A VAL* 3.8 19.3 - - + -
135A GLU* 3.9 25.6 - - + +
76B ARG* 3.5 37.5 - - + +
77B PRO* 3.4 29.2 - - + +
78B ILE 3.1 0.2 - - - -
79B SER* 1.3 82.9 - - - +
81B LEU* 1.3 65.4 + - - +
82B ASN 3.1 4.0 - - - +
83B LYS* 2.8 25.1 + - + +
84B ILE* 2.8 27.5 + - + +
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Residues in contact with LEU 81 (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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78B ILE 3.2 15.7 + - - +
79B SER 3.4 1.4 + - - +
80B ILE* 1.3 75.1 - - - +
82B ASN* 1.3 82.1 + - - +
84B ILE* 3.6 10.8 - - - +
85B VAL* 2.9 42.8 + - + +
118B GLU* 4.9 7.2 - - + +
121B LEU* 3.5 48.0 - - + +
122B LEU* 4.0 24.2 - - + +
125B MSE 4.0 24.0 - - + -
321B THR* 5.5 2.7 - - + -
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Residues in contact with ASN 82 (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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135A GLU 2.8 26.3 + - - +
136A LEU* 3.5 22.8 + - - +
138A GLY 3.4 25.3 + - - +
139A PRO* 3.6 5.1 - - - +
140A GLY* 3.7 10.5 - - - +
80B ILE 2.9 1.2 + - - -
81B LEU* 1.3 99.9 - - - +
83B LYS* 1.3 58.3 + - - +
85B VAL* 3.6 6.2 + - - +
86B ASN* 2.9 27.7 + - - +
118B GLU* 5.7 0.2 - - - +
321B THR* 5.3 6.4 - - - +
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Residues in contact with LYS 83 (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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135A GLU* 3.1 32.5 + - + +
139A PRO 4.1 5.1 + - - +
140A GLY* 4.5 1.5 - - - -
141A LYS* 4.4 22.2 + - - +
76B ARG* 3.8 11.2 - - - +
80B ILE* 2.8 27.1 + - + +
82B ASN* 1.3 77.1 - - - +
84B ILE* 1.3 56.9 + - - +
86B ASN* 2.8 7.9 + - - +
87B ASP* 2.7 57.3 + - - +
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Residues in contact with ILE 84 (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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11B ILE* 5.2 1.3 - - + -
72B HIS 4.0 6.0 - - - +
73B VAL* 3.9 30.3 - - + +
76B ARG* 3.4 40.7 + - + +
77B PRO 3.7 24.7 - - - +
78B ILE* 4.9 0.4 - - - -
80B ILE* 2.8 26.0 + - + +
81B LEU* 3.6 9.2 - - - +
83B LYS* 1.3 73.9 - - - +
85B VAL* 1.3 63.5 + - - +
87B ASP* 3.1 17.5 + - - +
88B MSE 3.2 11.8 + - - +
92B TYR* 4.9 1.6 + - - +
117B LEU* 4.2 3.8 - - + -
121B LEU* 3.8 28.0 - - + -
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Residues in contact with VAL 85 (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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81B LEU* 2.9 25.8 + - + +
82B ASN* 3.7 5.6 - - - +
84B ILE* 1.3 73.8 - - - +
86B ASN* 1.3 57.9 + - + +
88B MSE 3.3 7.3 + - - +
89B HIS* 3.1 35.5 + - + +
114B VAL* 3.6 22.7 - - + +
117B LEU* 4.9 3.8 - - + -
118B GLU* 3.6 46.4 - - + +
121B LEU* 3.7 17.3 - - + -
319B THR* 5.2 0.9 - - + -
321B THR* 5.7 0.2 - - - +
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Residues in contact with ASN 86 (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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139A PRO* 3.3 38.5 - - + +
142A GLN* 4.0 13.3 + - - +
82B ASN 2.9 17.2 + - - +
83B LYS* 2.8 11.2 + - + +
85B VAL* 1.3 71.2 - - - +
87B ASP* 1.3 69.8 + - - +
89B HIS* 3.3 17.9 + - - +
90B ASN* 3.1 37.2 + - - +
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Residues in contact with ASP 87 (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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76B ARG* 2.7 39.3 + - - +
83B LYS* 2.7 35.1 + - - +
84B ILE 3.5 6.1 - - - +
86B ASN* 1.3 76.0 - - - +
88B MSE 1.3 57.0 + - - +
90B ASN* 3.0 14.5 + - - +
91B GLY 2.9 23.7 + - - -
92B TYR* 3.9 20.9 - - + +
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Residues in contact with MSE 88 (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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65B ALA* 3.5 28.5 - - + +
66B LEU* 3.7 11.9 - - + -
69B ALA* 3.7 7.6 - - + -
84B ILE 3.2 8.5 + - - +
85B VAL* 3.6 8.5 - - - +
87B ASP* 1.3 75.4 - - - +
89B HIS* 1.3 58.1 + - - +
90B ASN 3.2 0.5 + - - -
91B GLY 3.4 1.4 + - - -
92B TYR* 3.2 27.2 + - + +
110B ARG* 2.8 47.1 + - - +
113B ALA* 3.5 29.8 - - + -
114B VAL* 3.8 24.0 - - + +
117B LEU* 3.7 29.8 - - + -
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Residues in contact with HIS 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 VAL* 3.1 28.6 + - + +
86B ASN* 3.4 21.3 - - - +
88B MSE 1.3 75.0 - - - +
90B ASN* 1.3 66.5 + - - +
107B PHE* 5.8 4.2 - - - -
110B ARG* 4.3 11.3 + - - +
111B VAL* 4.3 22.6 - - + +
114B VAL* 3.9 18.7 - - + +
318B TRP 5.8 0.4 - - - -
319B THR* 3.6 31.9 + - + +
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Residues in contact with ASN 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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142A GLN* 5.9 0.4 + - - -
86B ASN* 3.1 31.1 + - - +
87B ASP* 3.0 14.7 + - - +
89B HIS* 1.3 84.0 - - - +
91B GLY* 1.3 58.7 + - - +
92B TYR 3.9 1.9 + - - +
110B ARG* 5.8 0.2 - - - -
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Residues in contact with GLY 91 (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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68B GLU* 3.9 7.4 - - - +
87B ASP 2.9 15.3 + - - -
88B MSE 3.4 1.5 + - - -
90B ASN* 1.3 75.1 - - - +
92B TYR* 1.3 79.7 + - - +
110B ARG* 3.4 29.0 + - - -
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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