Contacts of the helix formed by residues 111 - 121 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ALA* 5.0 4.9 - - + -
90A VAL* 6.3 0.2 - - + -
110A ALA* 1.3 71.1 - - - +
112A GLU* 1.3 62.4 + - + +
113A PRO* 3.2 39.2 - - + +
114A SER* 2.8 37.6 + - - +
115A GLN 3.2 3.1 + - - -
154A GLU* 2.8 16.0 + - - +
158A SER* 3.2 24.8 + - - +
185A ASP* 4.9 0.2 - - - +
372A ARG* 6.2 1.3 - - - -
700A P3F 2.8 124.9 + + + +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA 3.2 5.5 + - - -
111A TYR* 1.3 72.7 - - + +
113A PRO* 1.3 68.9 - - + +
115A GLN* 3.0 12.5 + - + +
116A ASP* 2.8 48.1 + - - +
158A SER* 5.3 0.2 - - - -
358A ILE* 3.4 46.0 - - + +
700A P3F 5.0 9.8 - - + +
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Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 5.0 13.0 - - + -
111A TYR* 3.2 32.1 - - + -
112A GLU* 1.3 93.7 - - + +
114A SER* 1.3 55.0 + - - +
116A ASP* 3.8 9.5 - - + +
117A PHE* 2.9 31.0 + - - +
700A P3F 2.7 48.2 - - + -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 3.4 37.4 - - - +
106A MET* 4.0 16.7 - - - +
110A ALA* 4.4 6.7 - - - -
111A TYR* 2.8 34.2 + - - +
113A PRO* 1.3 73.8 - - - +
115A GLN* 1.3 61.6 + - - +
117A PHE* 3.4 7.0 + - - +
118A CYS* 3.4 24.3 + - - -
152A PHE* 4.6 5.8 - - - -
154A GLU* 4.9 0.2 + - - -
185A ASP* 4.7 2.1 + - - -
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Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ASN 3.2 13.5 + - - -
110A ALA* 3.0 33.4 + - + +
111A TYR 3.2 2.2 + - - +
112A GLU* 3.0 12.4 + - + +
114A SER* 1.3 77.6 - - - +
116A ASP* 1.3 61.1 + - - +
118A CYS* 3.1 7.3 + - - +
119A SER* 2.9 27.2 + - - -
131A TRP* 3.5 32.9 - - + -
358A ILE* 2.9 33.3 + - - +
359A ARG* 4.0 1.6 - - - +
360A PRO* 3.1 29.1 - - - +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 2.8 45.4 + - - +
113A PRO* 3.8 9.2 - - + +
115A GLN* 1.3 72.4 - - - +
117A PHE* 1.3 67.7 + - - +
119A SER* 3.5 10.3 + - - -
120A LYS* 2.8 57.4 + - + +
700A P3F 5.8 1.9 - - - -
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 5.4 1.1 - - + -
91A ALA* 3.2 52.3 - - + +
94A ILE* 3.7 24.7 - - + -
95A LEU* 4.3 12.6 - - + -
113A PRO 2.9 18.1 + - - +
114A SER* 3.6 5.8 - - - +
116A ASP* 1.3 74.9 - - - +
118A CYS* 1.3 62.6 + - - +
121A ILE* 2.9 62.5 + - + +
122A LEU* 3.1 44.3 + - + -
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Residues in contact with CYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 4.3 2.0 - - - -
104A VAL* 4.3 6.3 - - - -
106A MET* 3.5 33.4 - - - -
114A SER 3.4 5.4 + - - -
115A GLN 3.1 9.5 + - - +
117A PHE* 1.3 86.0 - - - +
119A SER* 1.3 61.8 + - - +
122A LEU* 3.3 28.4 - - - +
123A SER* 3.3 22.9 + - - -
127A VAL 5.1 0.2 - - - +
129A THR* 3.4 34.5 + - + +
131A TRP* 4.2 2.2 - - + -
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLN 2.9 18.4 + - - -
116A ASP* 3.4 14.2 + - - -
118A CYS* 1.3 75.0 - - - +
120A LYS* 1.3 64.3 + - - +
123A SER* 2.6 26.3 + - - -
129A THR* 5.8 1.6 - - - -
131A TRP* 4.9 10.5 - - - -
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASP* 2.8 48.0 + - + +
119A SER* 1.3 81.2 - - - +
121A ILE* 1.3 70.3 + - + +
123A SER* 4.0 3.9 + - - -
124A LYS* 3.8 19.8 + - - +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 5.9 1.1 - - + -
117A PHE* 2.9 47.3 + - + +
120A LYS* 1.3 87.9 - - + +
122A LEU* 1.3 66.8 + - - +
123A SER 3.2 1.1 - - - -
124A LYS* 3.2 42.4 + - - +
125A LEU* 3.5 21.0 - - + +
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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