Contacts of the helix formed by residues 113 - 124 (chain A) in PDB entry 2FQ4
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 ASP 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PHE* 3.6 21.7 - - + -
31A LYS* 5.7 4.5 - - - +
56A LYS* 5.2 2.6 - - - -
57A ALA* 5.8 0.2 - - - +
109A GLU* 3.2 14.0 + - + +
110A GLY* 3.3 12.4 + - - +
112A PHE* 1.3 81.1 - - + +
114A SER* 1.3 61.9 + - - +
115A LYS* 3.0 41.1 + - - +
116A LEU* 3.1 17.7 + - + +
117A ALA 3.2 15.2 + - - -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLY 4.2 2.2 + - - -
112A PHE 4.1 1.0 + - - -
113A ASP* 1.3 71.0 + - - +
115A LYS* 1.3 67.0 + - - +
117A ALA* 3.7 9.5 - - - +
118A GLU* 3.0 29.3 + - - +
121A ARG* 5.4 2.7 + - - -
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Residues in contact with LYS 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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55A ASN* 5.5 14.4 + - + +
56A LYS* 6.5 0.4 - - - -
57A ALA* 4.2 9.2 - - + -
113A ASP* 3.0 25.6 + - - +
114A SER* 1.3 85.7 - - - +
116A LEU* 1.3 61.1 + - - +
118A GLU* 3.5 7.4 + - - +
119A GLU* 3.2 23.7 + - - +
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Residues in contact with LEU 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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30A PHE* 3.7 40.2 - - + -
57A ALA* 3.8 9.5 - - + +
61A MSE 4.2 28.7 - - + -
106A LEU* 3.4 30.7 - - + +
109A GLU* 3.6 22.2 - - + -
110A GLY* 4.0 2.0 - - - +
113A ASP* 3.1 23.5 + - + +
115A LYS* 1.3 74.1 - - - +
117A ALA* 1.3 65.1 + - - +
119A GLU* 3.0 5.9 + - - +
120A TYR* 2.9 31.3 + - + -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLY 3.9 7.9 - - - +
113A ASP 3.2 10.8 + - - +
114A SER* 3.7 11.2 - - - +
115A LYS 3.4 0.2 - - - -
116A LEU* 1.3 74.7 - - - +
118A GLU* 1.3 66.8 + - - +
120A TYR* 3.3 30.1 + - + +
121A ARG* 3.0 54.3 + - - +
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Residues in contact with GLU 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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114A SER 3.0 14.2 + - - +
115A LYS* 3.5 11.7 - - - +
117A ALA* 1.3 75.3 - - - +
119A GLU* 1.3 71.2 + - - +
121A ARG* 3.7 14.3 + - - +
122A VAL* 3.2 51.5 + - + +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASN* 4.7 4.3 + - - +
57A ALA* 3.8 5.4 - - + -
58A ALA* 3.6 32.4 - - - +
61A MSE 3.6 16.1 - - + +
115A LYS 3.2 11.1 + - - +
116A LEU 3.0 10.4 + - - +
118A GLU* 1.3 86.9 - - + +
120A TYR* 1.3 57.3 + - - +
122A VAL* 4.1 3.8 - - - +
123A ARG* 1.9 92.8 + - - +
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Residues in contact with TYR 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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61A MSE 4.0 23.3 - - + -
103A ILE* 6.1 1.8 - - + -
106A LEU* 3.4 32.5 - - + -
107A VAL* 3.7 23.8 + - + +
110A GLY* 3.3 21.9 - - - -
111A GLN* 4.1 5.4 + - - -
116A LEU* 2.9 29.0 + - + -
117A ALA* 3.4 38.2 - - + +
119A GLU* 1.3 77.2 - - - +
121A ARG* 1.3 71.2 + - + +
124A TYR* 3.0 8.8 + - + +
125A PHE* 3.0 53.9 + + + -
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Residues in contact with ARG 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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114A SER* 5.4 3.2 + - - -
117A ALA* 3.0 44.4 + - - +
118A GLU* 3.7 13.6 + - - +
119A GLU 3.3 0.2 - - - -
120A TYR* 1.3 90.8 + - + +
122A VAL* 1.3 61.3 + - + +
125A PHE* 3.8 10.7 - - + +
126A GLN* 2.8 31.9 + - - +
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Residues in contact with VAL 122 (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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118A GLU* 3.2 42.4 + - + +
119A GLU* 5.0 4.0 - - - +
121A ARG* 1.3 79.5 - - + +
123A ARG* 1.3 78.6 + - + +
126A GLN* 3.1 32.8 + - - +
127A PRO* 3.3 12.2 - - - +
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A TRP 5.9 0.2 + - - -
53A TRP* 4.2 6.5 - - - -
54A PRO* 5.3 4.2 - - - +
58A ALA* 3.5 21.0 + - - +
61A MSE 3.9 15.7 - - + -
62A ASP* 2.8 49.9 + - - +
65A LEU* 3.5 25.5 - - + +
119A GLU* 1.9 54.5 + - - +
122A VAL* 1.3 90.4 - - + +
124A TYR* 1.3 58.0 + - - +
127A PRO* 3.5 13.9 - - - +
128A ARG* 4.0 3.8 + - - -
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Residues in contact with TYR 124 (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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61A MSE 4.3 16.2 - - + -
64A PHE* 4.5 1.8 - + - -
65A LEU* 4.0 10.1 - - + -
70A ALA* 4.2 1.1 - - + -
91A LEU* 3.4 23.8 - - + +
94A PHE* 3.5 31.9 - + - -
95A LEU* 3.7 4.0 - - - +
103A ILE* 3.9 25.6 - - + -
120A TYR* 3.0 13.7 + - + +
123A ARG* 1.3 80.0 - - - +
125A PHE* 1.3 99.6 + + + +
126A GLN 3.5 0.4 - - - -
127A PRO* 3.2 4.3 - - - +
128A ARG* 2.9 72.1 + - + +
163A PHE* 4.4 8.1 - + - -
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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