Contacts of the helix formed by residues 101 - 116 (chain A) in PDB entry 3AP1
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 ARG 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A GLU* 4.0 21.2 + - + +
100A THR* 1.3 76.0 + - - +
102A ILE* 1.3 61.1 + - - +
103A ILE 3.3 1.8 - - - -
104A PRO* 3.2 18.5 - - - +
105A ARG* 3.4 14.2 + - - +
159A ASP* 2.8 16.2 + - - -
119B GLU* 2.9 31.0 + - - +
122B ARG* 3.5 53.7 - - - +
123B LEU* 4.0 14.8 - - + -
126B ALA* 5.7 0.4 - - - -
1003S PHE* 3.6 6.6 - - - -
1004S GLU 2.8 23.4 + - - -
1005S ASP 3.0 22.8 + - - -
1007S GLU* 3.2 14.8 + - - +
1008S PHE* 5.2 1.9 - - - -
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Residues in contact with ILE 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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100A THR* 2.6 18.7 + - - +
101A ARG* 1.3 71.5 - - - +
103A ILE* 1.3 62.4 + - - +
105A ARG* 3.6 9.8 - - - +
106A VAL* 2.9 31.1 + - + +
140A PHE* 3.7 19.1 - - + -
144A VAL* 3.9 35.2 - - + -
109B MET* 3.8 25.8 - - + -
113B TRP* 3.5 33.9 - - + +
123B LEU* 4.5 5.6 - - + +
128B VAL* 4.2 10.8 - - + -
133B LEU* 4.2 11.7 - - + -
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Residues in contact with ILE 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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72A PHE* 5.5 4.9 - - + -
100A THR* 3.3 12.3 + - - +
102A ILE* 1.3 78.4 - - + +
104A PRO* 1.4 70.3 - - + +
106A VAL* 3.3 7.5 - - + +
107A LEU* 3.0 41.4 + - + +
140A PHE* 5.5 0.7 - - + -
141A ILE* 3.8 30.1 - - + +
144A VAL* 4.2 20.4 - - + -
145A ILE* 3.7 21.1 - - + -
157A ASN* 3.5 31.0 - - - +
159A ASP* 4.3 1.1 - - - +
162A THR* 3.9 11.7 - - + -
169A LEU* 5.6 0.4 - - + -
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Residues in contact with PRO 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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101A ARG* 3.2 18.4 - - - +
103A ILE* 1.4 95.2 - - + +
105A ARG* 1.3 54.4 + - - +
107A LEU* 3.4 7.2 + - + +
108A ALA* 2.9 30.1 + - - +
159A ASP* 3.5 36.1 - - + +
161A PHE* 5.3 4.7 - - + +
162A THR* 4.0 15.3 - - + +
1008S PHE* 4.2 22.9 - - + +
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Residues in contact with ARG 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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101A ARG 3.4 12.2 + - - +
102A ILE* 3.6 14.1 - - - +
103A ILE 3.2 0.6 - - - -
104A PRO* 1.3 78.3 - - - +
106A VAL* 1.3 62.9 + - - +
108A ALA* 3.2 4.9 + - - +
109A MET* 3.0 37.1 + - + +
109B MET* 3.9 28.8 - - - +
113B TRP* 3.9 22.7 - - - +
119B GLU* 3.9 15.8 + - - -
1007S GLU* 2.5 31.1 + - - -
1008S PHE* 3.5 41.2 - - + -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 2.9 23.5 + - + +
103A ILE* 3.3 14.4 - - - +
105A ARG* 1.3 72.3 - - - +
107A LEU* 1.3 60.6 + - - +
109A MET* 3.3 11.3 + - + +
110A ARG* 2.9 25.1 + - - +
113A TRP* 5.6 0.7 - - - -
137A MET* 3.5 27.1 - - + +
140A PHE* 3.6 44.2 - - + -
141A ILE* 4.4 7.4 - - + -
106B VAL* 5.6 3.8 - - + -
109B MET* 3.8 24.2 - - + -
140B PHE* 6.1 2.7 - - + -
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Residues in contact with LEU 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 ILE* 3.0 38.1 + - + +
104A PRO* 3.7 5.4 - - + +
106A VAL* 1.3 77.6 - - - +
108A ALA* 1.3 61.6 + - - +
110A ARG* 3.9 1.7 - - - +
111A GLN* 3.0 25.3 + - - +
137A MET* 3.9 12.1 - - + -
141A ILE* 4.1 6.3 - - + -
162A THR* 3.9 17.7 - - + -
165A SER* 4.4 21.1 - - - +
168A TYR* 3.7 36.8 - - + -
169A LEU* 3.8 25.6 - - + -
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Residues in contact with ALA 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 PRO 2.9 11.5 + - - +
105A ARG 3.6 4.5 - - - +
107A LEU* 1.3 75.8 - - - +
109A MET* 1.3 62.5 + - - +
111A GLN* 3.4 7.3 + - - +
112A ALA* 3.0 24.7 + - - +
1008S PHE* 3.5 37.2 - - + -
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Residues in contact with MET 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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105A ARG* 3.0 26.2 + - + +
106A VAL* 3.6 11.9 - - + +
108A ALA* 1.3 76.7 - - + +
110A ARG* 1.3 62.0 + - - +
112A ALA* 3.3 7.0 + - - +
113A TRP* 3.1 58.9 + - + +
105B ARG* 4.1 24.9 - - + +
106B VAL* 4.1 15.7 - - + -
109B MET* 3.6 29.2 - - + +
1008S PHE* 5.8 3.6 - - + -
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Residues in contact with ARG 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 VAL 2.9 17.0 + - - +
107A LEU 3.9 2.7 - - - +
109A MET* 1.3 73.5 - - - +
111A GLN* 1.3 69.5 + - - +
113A TRP* 3.2 29.3 + - + +
114A SER* 2.6 31.5 + - - +
130A ASP* 3.0 25.9 + - - -
133A LEU* 3.8 25.5 - - + +
134A ASP* 3.1 19.2 + - - -
137A MET* 3.6 27.4 - - + -
168A TYR* 2.9 39.4 + - - -
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Residues in contact with GLN 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 LEU 3.0 17.3 + - - +
108A ALA* 3.5 8.7 - - - +
110A ARG* 1.3 80.6 - - - +
112A ALA* 1.3 59.3 + - - +
114A SER* 3.3 6.6 + - - -
115A LYS* 2.9 48.8 + - + +
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Residues in contact with ALA 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 ALA 3.0 13.8 + - - +
109A MET* 3.3 10.5 + - - +
111A GLN* 1.3 76.2 - - - +
113A TRP* 1.3 62.1 + - - +
115A LYS* 3.7 10.2 - - - +
116A SER* 3.3 19.1 + - - -
1003T PHE* 3.8 24.7 - - + -
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Residues in contact with TRP 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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106A VAL 5.6 0.7 - - - -
109A MET* 3.1 53.4 + - + +
110A ARG* 3.6 26.7 - - + +
111A GLN 3.2 0.6 - - - -
112A ALA* 1.3 77.6 - - + +
114A SER* 1.3 60.1 + - - +
116A SER 3.7 0.9 - - - +
119A GLU* 3.6 14.8 - - + +
120A LYS* 3.6 22.2 + - - -
123A LEU* 3.9 16.1 - - + +
133A LEU* 3.7 22.4 - - + -
137A MET* 5.3 1.3 - - - -
102B ILE* 3.6 35.9 - - + -
105B ARG* 3.4 39.9 - - + +
106B VAL* 4.3 12.3 - - + -
140B PHE* 4.3 12.1 - + - -
1003T PHE* 3.5 18.3 - + - -
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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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110A ARG* 2.6 33.1 + - - -
111A GLN* 3.3 10.3 + - - -
113A TRP* 1.3 73.9 - - - +
115A LYS* 1.3 66.9 + - - +
116A SER 3.2 8.8 + - - +
117A GLY* 4.6 0.7 + - - -
120A LYS* 4.1 27.0 - - - +
123A LEU* 5.7 0.5 - - - +
130A ASP* 3.8 12.2 + - - -
133A LEU* 4.3 5.9 - - - +
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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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111A GLN* 2.9 36.2 + - + +
112A ALA* 3.4 10.3 + - - +
114A SER* 1.3 76.9 - - - +
116A SER* 1.3 58.8 + - - +
117A GLY* 3.4 3.5 + - - -
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Residues in contact with SER 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 ALA 3.3 11.6 + - - -
113A TRP 3.7 1.2 - - - +
114A SER 3.2 1.5 - - - -
115A LYS* 1.3 76.1 - - - +
117A GLY* 1.3 64.7 + - - +
118A ARG 3.6 2.3 + - - -
119A GLU* 3.1 29.7 + - - +
120A LYS* 2.9 23.4 + - - +
1001T GLU* 3.4 9.7 + - - -
1002T ASP* 3.0 37.0 + - - -
1003T PHE* 4.1 0.7 - - - -
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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