Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 1AP5
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 SER 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.9 8.1 - - - +
98A LYS* 4.3 11.9 - - - -
101A PHE* 3.1 6.5 + - - +
102A GLY* 1.3 77.0 - - - +
104A PHE* 1.3 63.7 + - - +
105A ASP* 3.7 6.7 + - - +
106A LYS* 3.3 31.1 + - - +
107A PHE* 3.3 21.3 + - - +
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Residues in contact with PHE 104 (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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87A GLY 3.6 20.4 - - - -
88A GLU* 3.8 35.4 - - + +
89A PRO* 3.3 20.9 - - + -
94A LEU* 3.7 29.2 - - + -
97A ILE* 4.2 8.7 - - + +
98A LYS* 4.7 4.0 - - - +
103A SER* 1.3 75.6 - - - +
105A ASP* 1.3 65.7 + - - +
107A PHE* 3.4 17.9 + + - +
108A LYS* 3.0 53.7 + - - +
181A TRP* 5.1 4.0 - + - -
186A TRP* 3.8 22.9 - + - -
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Residues in contact with ASP 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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88A GLU* 4.5 6.2 - - - +
103A SER* 3.3 6.2 + - - +
104A PHE* 1.3 90.5 - - - +
106A LYS* 1.3 58.7 + - + +
107A PHE 3.2 0.2 - - - -
108A LYS* 3.6 27.0 + - - +
109A GLU* 3.0 30.5 + - - +
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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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101A PHE 3.2 25.8 - - - +
102A GLY* 4.3 10.0 - - - -
103A SER* 3.3 22.0 + - - +
105A ASP* 1.3 75.4 - - - +
107A PHE* 1.3 63.5 + - - +
109A GLU* 3.4 12.7 + - - +
110A LYS* 3.2 38.3 + - - +
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Residues in contact with PHE 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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97A ILE* 3.6 27.4 - - + -
101A PHE* 3.9 37.2 - + + +
103A SER 3.3 6.1 + - - +
104A PHE* 3.5 25.4 - + - +
105A ASP 3.2 0.2 - - - -
106A LYS* 1.3 79.9 - - - +
108A LYS* 1.3 64.3 + - + +
110A LYS* 3.4 3.1 + - - +
111A LEU* 3.1 45.7 + - + +
126A LEU* 3.3 31.4 - - + -
137A ILE* 4.4 3.1 - - + -
156A LEU* 4.1 15.0 - - + -
181A TRP* 3.9 19.3 - + - -
186A TRP* 4.0 16.2 - + - -
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Residues in contact with LYS 108 (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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104A PHE* 3.0 40.4 + - - +
105A ASP* 3.6 27.1 + - - +
106A LYS 3.3 0.4 - - - -
107A PHE* 1.3 80.4 - - + +
109A GLU* 1.3 56.7 + - - +
111A LEU 3.5 0.2 + - - -
112A THR* 2.7 34.0 + - - +
178A LYS* 5.5 8.7 - - - +
181A TRP* 3.5 57.9 - - + +
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Residues in contact with GLU 109 (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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105A ASP 3.0 17.3 + - - +
106A LYS* 3.6 13.6 - - - +
108A LYS* 1.3 76.3 - - - +
110A LYS* 1.3 59.2 + - + +
112A THR* 3.4 7.9 + - - -
113A ALA* 2.9 28.0 + - + +
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Residues in contact with LYS 110 (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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100A ASP 5.5 0.8 + - - -
101A PHE* 4.2 33.9 + - + +
106A LYS* 3.2 23.3 + - - +
107A PHE 3.8 1.6 - - - +
108A LYS 3.3 0.2 - - - -
109A GLU* 1.3 74.3 - - + +
111A LEU* 1.3 61.7 + - - +
112A THR 3.0 1.1 - - - -
113A ALA* 3.2 6.5 + - - +
114A ALA* 2.9 30.8 + - - +
137A ILE* 3.6 17.3 - - + +
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Residues in contact with LEU 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 PHE* 3.1 37.9 + - + +
110A LYS* 1.3 76.6 - - - +
112A THR* 1.3 59.9 + - - +
114A ALA* 4.9 1.1 - - + -
115A SER* 2.7 45.0 + - - +
124A GLY* 4.0 2.7 - - - -
125A TRP 3.8 33.0 - - - +
126A LEU* 4.5 4.7 - - + -
137A ILE* 3.4 21.3 - - + +
156A LEU* 4.2 18.6 - - + +
158A ILE* 3.7 20.5 - - + +
181A TRP* 4.0 15.0 - - + -
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Residues in contact with THR 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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108A LYS* 2.7 23.8 + - - +
109A GLU* 3.4 8.2 - - - +
111A LEU* 1.3 77.9 - - - +
113A ALA* 1.3 57.4 + - - +
115A SER* 3.3 1.9 + - - -
116A VAL* 2.9 39.8 + - + +
174A PRO* 6.1 2.0 - - + -
177A LEU* 4.1 27.9 - - + +
178A LYS* 6.5 1.1 - - + -
181A TRP* 3.2 21.7 + - - -
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Residues in contact with ALA 113 (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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109A GLU 2.9 18.0 + - - +
110A LYS* 3.2 8.5 + - - +
112A THR* 1.3 77.1 - - - +
114A ALA* 1.3 56.6 + - - +
116A VAL* 3.9 7.6 - - - +
117A GLY* 3.1 24.9 + - - -
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Residues in contact with ALA 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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110A LYS 2.9 16.1 + - - +
111A LEU* 4.2 4.7 - - + +
113A ALA* 1.3 77.0 - - - +
115A SER* 1.3 58.8 + - - +
117A GLY* 3.7 5.1 + - - -
118A VAL* 3.3 21.7 + - - +
124A GLY* 5.1 1.1 - - - -
137A ILE* 3.7 24.5 - - + -
138A ALA 5.1 2.5 - - - +
139A ALA* 4.0 16.8 - - + +
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Residues in contact with SER 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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111A LEU* 2.7 28.6 + - - +
112A THR 3.9 2.2 - - - -
114A ALA* 1.3 73.0 - - - +
116A VAL* 1.3 63.6 + - - +
117A GLY 3.2 2.2 + - - -
118A VAL* 3.7 7.0 + - - -
124A GLY* 3.3 24.3 - - - -
158A ILE* 3.7 7.5 - - - +
160A VAL* 3.6 36.4 - - - +
173A ARG* 3.5 13.7 + - - -
177A LEU* 4.2 12.8 - - - -
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Residues in contact with VAL 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 THR* 2.9 23.2 + - + +
113A ALA* 4.3 7.4 - - - +
115A SER* 1.3 77.5 - - - +
117A GLY* 1.3 59.4 + - - +
118A VAL 3.5 0.4 - - - +
173A ARG* 3.5 22.8 + - + +
174A PRO* 4.0 38.1 - - + -
177A LEU* 4.3 14.6 - - + -
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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