Contacts of the helix formed by residues 107 - 115 (chain B) in PDB entry 1N1J
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B ARG* 4.1 10.7 + - - +
87B HIS* 4.2 17.7 - - + +
103B MET* 3.5 35.8 - - - +
104B ALA* 3.0 9.4 + - - +
106B THR* 1.3 92.2 - - - +
108B PHE* 1.3 59.9 + - + +
109B ASP 4.3 0.2 - - - -
120B ARG* 5.9 0.2 - - - +
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Residues in contact with PHE 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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79B GLU* 4.0 10.8 - - + -
83B ARG* 3.4 48.9 - - - +
104B ALA 3.6 3.4 + - - +
105B ILE 3.5 7.4 - - - +
106B THR 3.6 1.0 - - - -
107B LYS* 1.3 80.4 - - - +
109B ASP* 1.3 73.9 + - - +
110B GLN* 3.2 47.6 - - + -
111B PHE* 2.9 58.1 + + + -
112B ASP* 3.7 3.7 + - - +
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Residues in contact with ASP 109 (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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124A GLY 5.5 1.0 - - - +
107B LYS 4.3 0.6 + - - -
108B PHE* 1.3 82.2 - - - +
110B GLN* 1.3 84.4 + - - +
111B PHE 3.0 0.4 - - - -
112B ASP* 3.1 37.3 + - - +
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Residues in contact with GLN 110 (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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123A LEU 5.6 2.0 - - - +
124A GLY* 3.0 26.1 + - - +
125A PHE* 3.4 39.8 - - + +
127A SER* 4.0 15.8 + - - +
128A TYR* 3.9 15.8 + - - -
79B GLU* 5.1 2.9 - - - +
108B PHE* 3.1 40.0 - - + -
109B ASP* 1.3 85.4 + - - +
111B PHE* 1.3 64.7 + - + +
112B ASP 3.4 0.2 - - - -
113B PHE* 3.4 21.5 - - - -
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Residues in contact with PHE 111 (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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125A PHE* 5.6 0.4 - + - -
128A TYR* 5.5 0.4 - - - -
76B PHE* 3.8 30.7 - + - -
79B GLU* 4.2 5.8 - - + -
80B LEU* 3.6 46.9 - - + -
83B ARG* 3.7 17.9 - - + -
104B ALA 4.1 10.5 - - - -
105B ILE* 3.4 31.2 - - + +
108B PHE* 2.9 50.4 + + + +
110B GLN* 1.3 91.0 - - + +
112B ASP* 1.3 63.7 + - - +
113B PHE* 3.1 7.9 - + - -
114B LEU* 2.9 19.6 + - + +
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Residues in contact with ASP 112 (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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105B ILE 4.9 1.2 - - - +
106B THR 6.2 0.3 - - - -
108B PHE 3.7 3.1 + - - +
109B ASP* 3.1 36.5 + - - +
110B GLN 3.4 1.0 - - - -
111B PHE* 1.3 77.5 - - - +
113B PHE* 1.3 62.4 + - - +
114B LEU 3.0 1.8 + - - -
115B ILE* 3.1 39.3 + - + +
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Residues in contact with PHE 113 (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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90A GLU* 3.9 11.4 - - + +
91A PHE* 3.6 37.2 - + + -
94A PHE* 3.6 45.8 - + + -
125A PHE* 3.8 12.1 - + - -
76B PHE* 3.9 13.7 - + - -
110B GLN 3.4 24.5 - - - -
111B PHE* 3.1 3.4 + - - -
112B ASP* 1.3 77.7 - - - +
114B LEU* 1.3 96.3 + - + +
115B ILE 3.5 0.6 + - - -
116B ASP 5.0 1.2 + - - -
117B ILE* 4.0 11.3 - - - +
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Residues in contact with LEU 114 (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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87A CYS* 4.0 28.7 - - - -
90A GLU* 3.9 19.5 - - + -
76B PHE* 3.8 18.8 - - + -
80B LEU* 4.8 3.1 - - + -
105B ILE* 3.7 27.9 - - + +
111B PHE* 2.9 18.3 + - + +
113B PHE* 1.3 119.7 - - + +
115B ILE* 1.3 65.2 - - - +
116B ASP 3.3 2.9 - - - -
117B ILE* 2.9 20.6 + - + -
118B VAL* 3.0 12.1 + - - -
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Residues in contact with ILE 115 (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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105B ILE* 3.7 26.1 - - + +
106B THR* 5.2 14.4 - - + -
112B ASP* 3.1 39.2 + - + +
113B PHE 3.5 0.4 - - - -
114B LEU* 1.3 78.4 - - - +
116B ASP* 1.3 71.8 + - - +
118B VAL 3.7 0.4 - - - -
119B PRO* 3.4 26.2 - - + +
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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