Contacts of the helix formed by residues 101 - 112 (chain A) in PDB entry 3P8P
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 GLU 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ARG* 4.1 12.1 + - - +
71A LEU* 3.7 24.0 - - + +
73A ASP* 2.8 37.5 + - - +
74A CYS* 2.8 16.9 + - - +
76A PHE 4.8 0.3 - - - +
80A VAL* 3.2 22.8 - - + +
98A ARG* 3.0 50.6 + - - +
99A ARG 3.1 1.2 - - - -
100A LYS* 1.3 76.8 - - - +
102A VAL* 1.3 63.7 + - - +
103A ASP 3.2 0.8 + - - -
104A MET 3.8 2.2 + - - -
105A MET* 3.4 21.4 + - - +
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Residues in contact with VAL 102 (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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80A VAL* 4.6 8.3 - - + +
90A ILE* 3.2 25.8 - - + -
91A THR 3.2 26.7 - - - +
92A ARG* 5.3 0.2 - - - -
93A PRO* 4.5 9.2 - - + -
99A ARG 3.5 15.9 - - - +
100A LYS 3.1 0.2 - - - -
101A GLU* 1.3 77.0 - - - +
103A ASP* 1.3 62.3 + - - +
105A MET* 4.3 2.9 - - - -
106A LYS* 2.7 34.8 + - + +
118A GLU* 4.5 15.3 - - + +
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Residues in contact with ASP 103 (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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99A ARG 5.0 0.3 - - - +
100A LYS* 3.1 34.6 - - - +
102A VAL* 1.3 85.7 - - - +
104A MET* 1.3 59.1 + - - +
106A LYS* 4.0 3.3 - - - +
107A GLU* 3.0 28.6 + - - +
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Residues in contact with MET 104 (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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19A ARG* 3.5 38.8 - - - +
65A LEU* 3.6 19.9 - - + +
66A PRO* 3.5 36.8 - - + -
100A LYS 4.7 0.4 + - - -
101A GLU 3.8 2.2 + - - -
103A ASP* 1.3 79.4 - - - +
105A MET* 1.3 57.0 + - - +
107A GLU* 3.4 10.4 - - + +
108A ALA* 3.0 25.8 + - - +
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Residues in contact with MET 105 (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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17A VAL* 4.0 25.4 - - + -
65A LEU* 4.1 7.8 - - + +
77A VAL* 3.4 41.7 - - + +
80A VAL* 3.2 30.1 - - + -
81A ALA* 4.0 13.9 - - + -
90A ILE* 4.1 6.1 - - + -
101A GLU 3.4 17.9 + - - +
102A VAL* 3.7 4.7 - - - +
103A ASP 3.1 0.6 - - - -
104A MET* 1.3 77.4 - - - +
106A LYS* 1.3 64.8 + - - +
107A GLU 3.1 1.3 - - - -
108A ALA* 3.3 1.0 + - - -
109A LEU* 3.0 40.5 + - + +
277A VAL* 4.1 7.6 - - + -
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Residues in contact with LYS 106 (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 ILE* 4.0 23.7 - - + +
102A VAL* 2.7 23.9 + - + +
103A ASP* 4.0 3.6 - - - +
105A MET* 1.3 72.7 - - - +
107A GLU* 1.3 58.6 + - - +
109A LEU* 3.9 1.4 - - - +
110A GLU* 2.9 46.0 + - + +
116A ILE* 4.8 6.6 - - + +
118A GLU* 4.5 15.0 - - - +
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Residues in contact with GLU 107 (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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103A ASP 3.0 18.1 + - - +
104A MET* 3.4 15.7 - - + +
106A LYS* 1.3 79.9 - - - +
108A ALA* 1.3 61.3 + - - +
110A GLU* 3.4 14.2 + - - +
111A LYS* 3.1 21.7 + - - +
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Residues in contact with ALA 108 (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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17A VAL* 4.7 8.5 - - + -
63A VAL* 4.6 13.6 - - + +
65A LEU* 3.5 25.3 - - + +
104A MET 3.0 17.4 + - - +
105A MET* 3.3 6.7 + - - +
107A GLU* 1.3 73.9 - - - +
109A LEU* 1.3 66.5 + - + +
111A LYS* 3.1 10.4 + - - +
112A LEU* 3.1 24.6 + - + +
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Residues in contact with LEU 109 (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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17A VAL* 4.1 25.8 - - + -
81A ALA* 4.1 15.3 - - + -
83A VAL* 5.9 1.6 - - + -
88A ALA* 3.7 20.0 - - + -
90A ILE* 3.5 28.3 - - + -
105A MET* 3.0 20.1 + - + +
106A LYS 4.2 0.9 - - - +
108A ALA* 1.3 75.5 - - - +
110A GLU* 1.3 64.0 + - - +
112A LEU* 3.0 16.4 + - + +
114A LEU* 3.3 39.4 + - + +
116A ILE* 3.7 16.4 - - + -
277A VAL* 5.3 4.7 - - + -
279A ILE* 4.4 7.0 - - + -
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Residues in contact with GLU 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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106A LYS* 2.9 37.3 + - + +
107A GLU* 3.4 12.4 + - - +
108A ALA 3.1 0.2 - - - -
109A LEU* 1.3 76.7 - - - +
111A LYS* 1.3 56.9 + - - +
113A GLN* 2.9 22.3 + - - -
114A LEU 5.0 2.0 - - - -
116A ILE* 4.1 21.1 - - + -
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Residues in contact with LYS 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 GLU 3.1 10.4 + - - +
108A ALA* 3.1 12.1 + - - +
110A GLU* 1.3 78.5 - - - +
112A LEU* 1.3 60.5 + - + +
113A GLN* 3.2 3.8 + - - +
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Residues in contact with LEU 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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15A HIS* 3.9 31.0 - - + +
17A VAL* 4.4 17.9 - - + -
63A VAL* 4.3 24.5 - - + -
108A ALA 3.1 14.7 + - - +
109A LEU* 3.0 17.9 + - + +
110A GLU 3.0 1.6 - - - -
111A LYS* 1.3 81.4 - - + +
113A GLN* 1.3 62.5 + - - +
114A LEU* 3.2 12.9 + - + +
279A ILE* 4.7 13.0 - - + -
281A LYS* 2.9 34.7 + - + +
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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