Contacts of the helix formed by residues 112 - 120 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C LEU* 3.8 13.0 - - + -
71C ILE* 5.0 0.7 - - + -
79C HIS* 3.8 8.3 - - + -
81C ALA* 3.5 27.8 - - + -
94C ILE* 5.4 3.4 - - + -
96C ILE* 3.7 24.0 - - + -
104C LEU* 3.8 25.6 - - + -
105C VAL 3.2 45.8 - - - -
106C GLY* 3.6 12.3 - - - -
107C PRO 4.5 11.4 + - - -
110C GLY 3.2 1.0 - - - -
111C LEU* 1.3 78.8 - - + +
113C THR* 1.3 58.0 + - - +
114C TYR 3.5 1.6 - - - -
115C VAL* 3.5 23.6 - - + -
116C ALA* 2.8 31.4 + - - +
165C MSE 5.3 2.7 - - - -
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Residues in contact with THR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLY* 2.4 31.8 + - - -
111C LEU 3.2 1.4 + - - -
112C PHE* 1.3 78.9 - - - +
114C TYR* 1.3 63.6 + - + +
116C ALA* 3.8 3.0 - - - +
117C GLU* 3.1 35.6 + - - +
165C MSE 5.4 4.0 - - - -
166C VAL 3.8 1.4 + - - -
167C LYS* 3.4 19.2 - - + +
168C ILE* 3.0 40.4 + - + +
170C GLU* 3.2 23.8 - - - +
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Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TYR* 4.6 9.1 + - - -
64C ALA* 3.5 40.8 - - + +
65C TYR* 4.0 9.2 - + - -
68C LEU* 3.9 33.2 - - + +
111C LEU 4.9 1.2 + - - -
112C PHE 3.5 0.2 - - - -
113C THR* 1.3 77.7 - - + +
115C VAL* 1.3 67.2 + - - +
117C GLU* 3.4 9.1 + - - +
118C LYS* 3.2 22.2 + - - +
168C ILE* 3.6 29.6 - - + +
170C GLU* 3.1 39.2 - - + +
176C ILE* 4.8 28.4 + - + +
187C ASN* 5.3 5.0 + - - -
239C PHE* 6.0 3.4 - + - -
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA 5.1 0.8 + - - +
67C LEU* 4.3 23.6 - - + +
68C LEU* 4.7 6.7 - - - +
71C ILE* 3.8 37.2 - - + -
72C PRO* 4.9 3.4 - - + -
104C LEU* 4.0 7.2 - - + -
111C LEU 4.9 0.4 - - - +
112C PHE* 3.1 42.8 - - + +
114C TYR* 1.3 78.0 - - - +
116C ALA* 1.3 71.1 + - - +
118C LYS* 3.3 6.1 + - - +
119C LEU* 3.0 35.4 + - + +
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Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ILE* 4.2 19.5 - - + -
98C THR* 5.6 0.4 + - - -
104C LEU* 4.1 9.6 - - + -
112C PHE 2.8 22.1 + - - +
113C THR 3.8 3.8 - - - +
115C VAL* 1.3 77.9 - - - +
117C GLU* 1.3 57.3 + - + +
119C LEU* 3.8 2.0 - - - +
120C GLY* 2.8 33.3 + - - -
121C ILE* 3.8 24.0 + - + -
165C MSE 4.4 5.4 - - - -
167C LYS* 6.5 0.4 - - - -
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Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C THR 3.1 16.9 + - - +
114C TYR* 4.0 6.8 - - - +
115C VAL 3.3 0.4 - - - -
116C ALA* 1.3 74.4 - - + +
118C LYS* 1.3 67.6 + - - +
120C GLY* 3.2 12.7 + - - +
121C ILE* 5.5 3.1 - - + -
167C LYS* 3.1 36.8 + - - +
170C GLU* 2.6 39.4 - - - +
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 4.5 15.0 - - + -
72C PRO* 4.2 28.3 - - + -
114C TYR 3.2 12.1 + - - +
115C VAL 3.6 8.5 - - - +
117C GLU* 1.3 79.4 - - - +
119C LEU* 1.3 61.9 + - + +
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ILE* 3.9 5.6 - - + -
72C PRO* 4.3 27.1 - - + +
98C THR* 3.2 35.7 - - + +
99C LYS* 4.0 8.8 - - - +
100C SER* 5.8 0.3 - - - -
102C TYR* 3.6 41.5 - - + +
104C LEU* 4.5 4.5 - - + -
115C VAL* 3.0 36.9 + - + +
116C ALA* 4.2 2.7 - - - +
118C LYS* 1.3 80.3 - - + +
120C GLY* 1.3 64.1 + - - +
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Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ILE* 5.7 0.2 - - - +
98C THR* 3.3 8.1 + - - +
99C LYS* 3.1 23.1 + - - -
116C ALA 2.8 14.9 + - - -
117C GLU* 3.2 11.8 + - - -
119C LEU* 1.3 81.5 - - - +
121C ILE* 1.3 60.6 + - - -
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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