Contacts of the helix formed by residues 112 - 120 (chain B) in PDB entry 2F4N
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 PHE 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 3.5 27.1 - - + -
71B ILE* 4.7 0.9 - - + -
79B HIS 3.8 10.1 - - - -
81B ALA* 3.5 17.9 - - + -
94B ILE* 5.5 2.5 - - + -
96B ILE* 4.2 22.2 - - + -
104B LEU* 3.8 34.3 - - + -
105B VAL 3.1 35.0 - - - -
106B GLY* 3.9 10.3 - - - -
107B PRO 4.5 10.5 - - - -
110B GLY 3.1 0.8 - - - -
111B LEU* 1.3 81.6 - - + +
113B THR* 1.3 64.2 + - - +
114B TYR 3.4 2.5 - - - -
115B VAL* 3.1 24.3 - - + +
116B ALA* 2.7 26.2 + - - +
165B MSE 5.4 2.2 - - - -
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Residues in contact with THR 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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110B GLY* 2.6 35.5 + - - -
111B LEU 3.3 0.6 - - - -
112B PHE* 1.3 73.1 - - - +
114B TYR* 1.3 76.1 + - + +
116B ALA* 3.4 4.9 - - - +
117B GLU* 3.1 21.3 + - + +
165B MSE 5.3 3.7 - - - -
166B VAL 3.9 0.3 + - - -
167B LYS* 3.4 26.0 - - + -
168B ILE* 2.9 45.7 + - + +
170B GLU* 6.0 1.3 - - + -
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 4.5 9.8 - - - +
64B ALA* 3.7 35.4 - - + +
65B TYR* 4.2 9.2 - + + -
68B LEU* 3.7 34.7 - - + +
111B LEU 4.9 1.2 + - - -
112B PHE 3.4 0.6 - - - -
113B THR* 1.3 79.7 - - + +
115B VAL* 1.3 67.9 + - - +
116B ALA 3.2 0.2 + - - -
117B GLU* 3.3 5.7 + - - +
118B LYS* 3.0 24.6 + - - +
168B ILE* 3.7 41.0 - - + +
170B GLU* 5.3 9.9 - - + -
174B ARG* 5.8 0.7 + - - -
176B ILE* 4.1 31.9 + - + +
187B ASN* 4.8 6.4 + - - -
239B PHE* 6.0 1.6 - + - -
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Residues in contact with VAL 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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64B ALA 5.2 1.2 + - - +
67B LEU* 3.9 21.3 - - + +
68B LEU* 4.4 5.9 - - - +
71B ILE* 3.6 41.1 - - + -
72B PRO* 4.7 6.3 - - + -
104B LEU* 3.7 10.4 - - + +
111B LEU 5.0 0.4 + - - +
112B PHE* 3.1 43.9 - - + +
114B TYR* 1.3 79.2 - - - +
116B ALA* 1.3 64.7 + - - +
118B LYS* 3.7 5.1 + - - +
119B LEU* 3.2 29.1 + - + +
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Residues in contact with ALA 116 (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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96B ILE* 4.8 5.4 - - + -
98B THR* 5.3 1.5 + - - -
104B LEU* 4.7 7.4 - - + -
112B PHE* 2.7 29.2 + - + +
113B THR 3.4 4.9 - - - +
115B VAL* 1.3 73.2 - - - +
117B GLU* 1.3 56.2 + - - +
119B LEU* 3.7 0.8 - - - +
120B GLY* 2.7 39.6 + - - -
121B ILE* 4.0 25.8 - - + -
165B MSE 4.3 13.5 - - + -
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Residues in contact with GLU 117 (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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113B THR* 3.1 11.2 + - + +
114B TYR* 3.8 7.6 - - - +
116B ALA* 1.3 77.6 - - - +
118B LYS* 1.3 68.1 + - - +
120B GLY* 3.1 13.0 + - - -
121B ILE* 4.9 3.3 - - - +
167B LYS* 6.5 1.1 - - - -
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Residues in contact with LYS 118 (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 LEU* 4.3 18.4 - - + -
72B PRO* 4.2 27.8 - - + -
114B TYR 3.0 17.3 + - - +
115B VAL* 3.7 6.3 - - - +
117B GLU* 1.3 78.6 - - - +
119B LEU* 1.3 64.1 + - + +
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Residues in contact with LEU 119 (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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71B ILE* 3.8 24.9 - - + -
72B PRO* 4.5 26.5 - - + +
98B THR* 2.7 36.9 - - + +
99B LYS* 3.8 9.4 + - - +
100B SER* 4.6 2.0 + - - -
102B TYR* 3.8 45.1 - - + +
104B LEU* 5.6 2.7 - - + -
115B VAL* 3.2 18.6 + - + +
116B ALA 4.4 0.2 - - - +
118B LYS* 1.3 82.3 - - + +
120B GLY* 1.3 57.5 + - - +
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Residues in contact with GLY 120 (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 THR* 3.1 10.2 + - - +
99B LYS* 3.1 39.6 + - - -
116B ALA* 2.7 18.3 + - - -
117B GLU* 3.1 10.6 + - - -
118B LYS 3.4 0.4 + - - -
119B LEU* 1.3 73.7 - - - +
121B ILE* 1.3 60.4 + - - -
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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