Contacts of the helix formed by residues 109 - 121 (chain A) in PDB entry 2PRF
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 ALA 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ALA* 3.7 30.3 - - + +
16A VAL* 4.7 4.5 - - + -
87A ILE* 3.4 24.2 - - + -
100A TYR* 4.7 3.8 - - + -
104A ILE* 3.8 11.6 - - + +
105A GLN 3.4 6.3 + - - +
106A PRO 5.0 0.7 - - - +
107A GLY 3.1 0.6 - - - -
108A THR* 1.3 78.3 - - - +
110A ALA* 1.3 64.9 + - - +
111A ASN 3.1 1.6 - - - -
112A VAL* 4.1 0.5 - - - +
113A VAL* 3.1 30.6 + - + +
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Residues in contact with ALA 110 (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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78A TYR* 5.1 16.2 - - + -
87A ILE* 4.2 10.9 - - + +
106A PRO 3.3 20.5 + - - +
107A GLY* 3.3 7.4 + - - +
109A ALA* 1.3 79.9 - - - +
111A ASN* 1.3 63.5 + - - +
113A VAL* 4.0 6.2 - - - +
114A GLU* 3.1 35.7 + - + +
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Residues in contact with ASN 111 (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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107A GLY* 3.0 24.9 + - - +
108A THR* 4.1 7.0 - - - +
109A ALA 3.1 0.2 - - - -
110A ALA* 1.3 83.9 + - - +
112A VAL* 1.3 67.1 + - + +
114A GLU* 3.3 12.8 + - - +
115A LYS* 3.3 17.8 + - - +
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Residues in contact with VAL 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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10A LEU* 5.4 7.9 - - + -
14A GLY 4.3 14.4 - - - +
15A ALA* 4.2 17.3 - - + -
108A THR* 3.3 20.4 - - + +
109A ALA 3.5 3.9 + - - +
111A ASN* 1.3 79.1 - - + +
113A VAL* 1.3 62.9 + - + +
114A GLU 3.1 0.9 + - - -
115A LYS* 3.4 4.1 + - + +
116A LEU* 3.2 38.0 + - + +
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Residues in contact with VAL 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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2A TRP* 3.6 25.0 - - + +
10A LEU* 5.3 4.5 - - + -
15A ALA* 5.4 3.6 - - + -
16A VAL* 5.9 4.0 - - + -
78A TYR* 4.8 3.7 - - + -
87A ILE* 3.4 31.0 - - + -
89A VAL* 3.8 10.5 - - + +
96A LEU* 3.4 27.6 - - + -
98A GLY* 5.9 2.2 - - - -
109A ALA* 3.1 20.7 + - + +
110A ALA* 4.4 3.8 - - - +
112A VAL* 1.3 79.0 - - + +
114A GLU* 1.3 61.4 + - - +
117A ALA* 3.4 21.6 + - - +
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Residues in contact with GLU 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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76A SER* 5.6 0.2 + - - -
78A TYR* 4.1 25.5 + - + +
110A ALA* 3.1 24.3 + - + +
111A ASN* 3.6 8.3 - - - +
112A VAL 3.1 0.6 - - - -
113A VAL* 1.3 80.2 - - - +
115A LYS* 1.3 62.7 + - + +
117A ALA* 4.1 3.1 - - - +
118A ASP* 3.0 41.4 + - - +
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Residues in contact with LYS 115 (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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111A ASN 3.3 13.8 + - - +
112A VAL* 4.1 4.5 - - - +
114A GLU* 1.3 79.6 - - + +
116A LEU* 1.3 72.5 + - + +
118A ASP* 2.9 29.6 + - + +
119A TYR* 3.3 25.6 + - + +
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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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1A SER* 4.4 9.2 + - - +
2A TRP* 4.1 17.0 - - + -
5A TYR* 3.1 43.5 - - + -
10A LEU* 3.6 19.3 - - + -
112A VAL* 3.2 30.0 + - + +
115A LYS* 1.3 80.5 - - + +
117A ALA* 1.3 63.6 + - - +
119A TYR* 3.1 34.5 + - + +
120A LEU* 3.7 4.3 + - - +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A TRP* 4.4 2.6 - - + -
76A SER* 6.0 2.0 - - - +
89A VAL* 5.0 5.8 - - + -
90A LYS 4.9 2.5 - - - +
91A THR* 4.1 22.9 - - + -
113A VAL 3.4 19.6 + - - +
114A GLU* 4.1 4.0 - - - +
115A LYS 3.1 0.4 - - - -
116A LEU* 1.3 74.4 - - - +
118A ASP* 1.3 56.5 + - - +
119A TYR 2.5 18.2 + - - -
120A LEU 2.5 15.5 + - - +
121A ILE* 2.7 28.4 - - + +
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Residues in contact with ASP 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 GLU* 3.0 31.1 + - - +
115A LYS* 2.9 25.3 + - + +
117A ALA* 1.3 75.3 - - - +
119A TYR* 1.3 67.0 + - + +
121A ILE* 3.3 18.7 + - - +
122A GLY 4.0 5.5 + - - -
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Residues in contact with TYR 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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5A TYR* 6.2 0.4 - - - -
115A LYS* 3.9 24.4 + - + +
116A LEU* 3.1 27.3 + - + +
117A ALA 2.5 7.5 + - - -
118A ASP* 1.3 83.3 - - + +
120A LEU* 1.3 64.4 + - + +
121A ILE 3.2 1.1 + - - -
122A GLY* 3.8 8.0 + - - -
123A GLN* 4.8 1.0 + - - +
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Residues in contact with LEU 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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1A SER* 3.4 36.8 - - - +
91A THR* 4.0 21.4 - - + +
92A SER* 3.7 20.2 - - - -
116A LEU 3.7 3.3 + - - +
117A ALA 2.5 11.1 + - - +
119A TYR* 1.3 76.9 - - + +
121A ILE* 1.3 63.6 + - - +
122A GLY 3.4 0.2 - - - -
123A GLN* 3.6 2.8 + - - +
124A GLY* 3.3 3.5 + - - -
125A PHE* 3.1 61.4 - - + -
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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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90A LYS 4.8 10.1 - - - +
91A THR* 5.0 1.1 - - + -
117A ALA* 2.7 53.6 - - + +
118A ASP* 3.3 18.6 - - - +
119A TYR 3.2 0.6 - - - -
120A LEU* 1.3 76.9 - - + +
122A GLY* 1.3 69.8 + - - +
123A GLN 2.7 5.2 + - - -
124A GLY* 3.0 16.3 + - - +
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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