Contacts of the helix formed by residues 111 - 121 (chain B) in PDB entry 2FQ6
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 TYR 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ALA* 5.1 5.1 - - + +
90B VAL* 6.0 0.2 - - + -
110B ALA* 1.3 73.4 - - - +
112B GLU* 1.3 71.6 + - + +
113B PRO* 3.3 34.5 - - + +
114B SER* 2.9 33.7 + - - +
115B GLN 3.3 3.6 + - - -
154B GLU* 2.9 14.2 + - - +
158B SER* 3.2 24.8 + - - +
159B ILE* 6.6 0.4 - - + -
185B ASP* 4.9 0.2 - - - +
372B ARG* 6.2 0.9 - - - -
700B P3F 3.0 120.9 + + + +
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Residues in contact with GLU 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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110B ALA 3.4 4.7 + - - -
111B TYR* 1.3 72.9 - - + +
113B PRO* 1.4 66.1 - - + +
115B GLN* 3.0 12.8 + - + +
116B ASP* 2.8 47.0 + - - +
158B SER* 5.3 0.4 - - - -
159B ILE* 6.5 0.2 - - + -
358B ILE* 3.4 47.4 - - + +
700B P3F 4.7 15.0 - - + -
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Residues in contact with PRO 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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87B ALA* 5.1 11.9 - - + -
111B TYR* 3.3 37.5 - - + +
112B GLU* 1.4 90.3 - - + +
114B SER* 1.3 55.8 + - - +
116B ASP* 3.8 9.9 - - + +
117B PHE* 2.9 29.6 + - - +
700B P3F 2.8 44.2 - - + -
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 3.6 37.7 - - - +
106B MET* 4.0 16.9 - - - +
110B ALA* 4.4 6.3 - - - -
111B TYR* 2.9 27.9 + - - +
113B PRO* 1.3 77.6 - - - +
115B GLN* 1.3 65.7 + - - +
117B PHE* 3.5 11.4 + - - +
118B CYS* 3.5 17.8 + - - -
152B PHE* 4.7 5.0 - - - -
154B GLU* 5.0 0.3 + - - -
185B ASP* 4.8 1.9 + - - -
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Residues in contact with GLN 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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106B MET* 4.1 0.9 - - - -
108B ASN 3.2 15.9 + - - -
110B ALA* 2.9 34.6 + - + +
111B TYR 3.8 2.2 - - - +
112B GLU* 3.0 12.0 + - + +
114B SER* 1.3 76.6 - - - +
116B ASP* 1.4 60.3 - - - +
118B CYS* 2.9 8.3 + - - +
119B SER* 2.9 26.3 + - - -
131B TRP* 3.6 33.0 - - + -
358B ILE* 3.1 29.5 + - - +
359B ARG* 4.1 1.2 - - - +
360B PRO* 3.2 27.4 - - - +
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Residues in contact with ASP 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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112B GLU* 2.8 45.0 + - - +
113B PRO* 3.9 8.2 - - + +
115B GLN* 1.4 72.0 - - - +
117B PHE* 1.3 61.7 + - - +
119B SER* 3.7 10.4 + - - -
120B LYS* 2.8 57.8 + - + +
700B P3F 5.2 4.7 - - - -
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Residues in contact with PHE 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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90B VAL* 5.4 1.1 - - + -
91B ALA* 3.3 51.1 - - + -
94B ILE* 3.6 22.4 - - + -
95B LEU* 4.2 12.8 - - + -
113B PRO 2.9 18.9 + - - +
114B SER* 3.6 5.8 - - - +
115B GLN 3.2 0.4 - - - -
116B ASP* 1.3 76.6 - - - +
118B CYS* 1.3 68.1 + - - +
121B ILE* 2.8 63.4 + - + +
122B LEU* 3.1 43.4 + - + -
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Residues in contact with CYS 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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94B ILE* 4.4 2.2 - - - -
104B VAL* 4.2 9.6 - - - -
106B MET* 3.6 25.6 - - - -
114B SER 3.5 14.5 + - - -
115B GLN 2.9 8.6 + - - +
117B PHE* 1.3 81.9 - - - +
119B SER* 1.3 62.8 + - - +
122B LEU* 3.4 29.0 - - + +
123B SER* 3.3 22.3 + - - -
127B VAL 4.9 0.3 - - - +
129B THR* 3.3 31.9 + - + +
131B TRP* 4.2 2.5 - - + -
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Residues in contact with SER 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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115B GLN 2.9 11.1 + - - -
116B ASP* 3.6 17.8 + - - -
118B CYS* 1.3 77.0 - - - +
120B LYS* 1.3 68.1 + - - +
123B SER* 2.6 25.5 + - - -
129B THR* 5.4 1.1 - - - -
131B TRP* 4.8 12.8 - - - -
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Residues in contact with LYS 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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116B ASP* 2.8 40.2 + - + +
119B SER* 1.3 87.9 + - - +
121B ILE* 1.3 70.8 + - + +
123B SER* 4.0 4.8 + - - -
124B LYS* 3.6 19.4 + - - +
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Residues in contact with ILE 121 (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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95B LEU* 5.8 1.8 - - + -
116B ASP 5.0 0.2 - - - +
117B PHE* 2.8 51.5 + - + +
120B LYS* 1.3 84.0 - - + +
122B LEU* 1.3 65.9 + - - +
123B SER 3.2 2.0 + - - -
124B LYS* 3.3 39.1 + - - +
125B LEU* 3.4 22.2 - - + +
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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