Contacts of the helix formed by residues 111 - 124 (chain A) in PDB entry 2P3Z
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LYS* 3.4 27.6 - - + +
108A CYS* 2.6 46.4 + - - +
109A VAL 3.3 1.0 - - - -
110A SER* 1.3 79.3 + - - +
112A ILE* 1.3 61.9 + - - +
113A LYS 3.5 2.0 - - - -
114A LEU* 3.5 19.4 + - + +
115A ILE* 3.0 25.9 + - - +
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Residues in contact with ILE 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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109A VAL 3.8 10.8 - - - +
110A SER 3.0 8.2 + - - +
111A ASP* 1.3 77.1 - - - +
113A LYS* 1.3 60.6 + - + +
115A ILE* 3.3 3.1 + - - +
116A HIS* 2.8 27.0 + - - +
141A ASP* 3.5 15.2 - - - +
144A LEU* 3.7 33.3 - - + +
145A TRP* 3.5 73.1 - - + +
148A PHE* 3.8 20.0 - - + -
310A THR* 3.8 3.4 - - - +
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Residues in contact with LYS 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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110A SER 4.9 0.4 + - - -
111A ASP 3.5 0.2 - - - -
112A ILE* 1.3 77.3 - - + +
114A LEU* 1.3 60.9 + - - +
116A HIS* 3.4 7.9 + - - +
117A ASP* 2.9 29.3 + - - +
145A TRP* 5.2 9.2 - - + -
310A THR* 4.1 24.7 - - + +
314A GLU* 6.0 1.3 - - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 3.8 29.6 - - + -
111A ASP* 3.5 23.5 + - + +
112A ILE 3.3 0.2 - - - -
113A LYS* 1.3 73.9 - - - +
115A ILE* 1.3 65.2 - - - +
117A ASP* 3.3 3.7 + - - +
118A GLN* 3.0 34.4 + - - +
52B TYR* 3.5 37.2 - - + +
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Residues in contact with ILE 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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10A ILE* 3.9 7.4 - - + -
103A PHE* 3.6 21.3 - - + +
104A ILE* 3.8 25.6 - - + +
107A LYS* 3.9 30.3 - - + -
111A ASP* 3.0 26.6 + - + +
112A ILE 3.8 0.2 - - - +
114A LEU* 1.3 74.9 - - - +
116A HIS* 1.3 57.8 + - - +
118A GLN* 3.3 6.7 + - - +
119A MET* 2.8 40.8 + - + +
144A LEU* 3.6 45.3 - - + -
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Residues in contact with HIS 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 ILE 2.8 18.1 + - - +
113A LYS* 3.6 9.6 - - - +
114A LEU 3.1 0.2 - - - -
115A ILE* 1.3 77.6 - - - +
117A ASP* 1.3 63.4 + - - +
119A MET* 3.3 10.6 + - + +
120A LEU* 3.1 49.0 + - + +
137A ILE* 4.2 12.6 - - + +
141A ASP* 3.4 28.0 - - + +
307A GLY* 2.7 30.4 + - - -
310A THR* 3.7 20.1 - - + +
311A THR* 3.1 21.7 + - - -
314A GLU* 5.4 3.1 - - - -
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Residues in contact with ASP 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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113A LYS 2.9 16.5 + - - +
114A LEU* 3.7 2.9 - - - +
116A HIS* 1.3 78.9 + - - +
118A GLN* 1.3 57.6 + - - +
120A LEU* 3.3 11.9 + - - +
121A GLY* 2.8 27.5 + - - -
49B MET* 4.6 0.7 - - - +
51B LYS* 3.1 26.3 + - - -
52B TYR* 2.6 28.1 + - - +
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Residues in contact with GLN 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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103A PHE* 3.6 27.0 - - + +
107A LYS* 2.9 31.8 + - - +
114A LEU* 3.0 27.8 + - + +
115A ILE* 3.8 3.7 - - - +
117A ASP* 1.3 75.7 - - - +
119A MET* 1.3 57.9 + - - +
122A ALA* 2.9 35.4 + - - +
49B MET* 3.6 15.8 - - + +
52B TYR* 3.7 43.1 - - + +
55B TYR* 3.9 14.3 - - - -
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Residues in contact with MET 119 (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 LEU* 3.7 41.3 - - + -
103A PHE* 4.8 7.0 - - + -
104A ILE* 4.7 0.7 - - + -
115A ILE* 2.8 27.3 + - + +
116A HIS* 3.6 26.0 - - + +
118A GLN* 1.3 79.4 - - - +
120A LEU* 1.3 53.2 + - - +
122A ALA 4.1 0.2 - - - -
123A THR* 2.7 39.4 + - - +
137A ILE* 4.0 33.9 - - + +
140A VAL* 3.6 35.4 - - + -
141A ASP* 4.1 7.9 - - - +
144A LEU* 4.7 1.3 - - + -
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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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116A HIS* 3.1 47.1 + - + +
117A ASP* 3.7 11.7 - - - +
119A MET* 1.3 72.3 - - - +
121A GLY* 1.3 66.0 + - - +
123A THR* 3.6 4.1 + - - +
124A MET* 3.1 31.7 + - + +
134A MET* 3.6 37.5 - - + -
137A ILE* 4.2 11.7 - - + -
284A THR* 4.9 10.8 - - + -
307A GLY* 5.7 0.7 - - - -
311A THR* 5.3 0.9 - - - +
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Residues in contact with GLY 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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117A ASP* 2.8 20.5 + - - -
120A LEU* 1.3 73.7 - - - +
122A ALA* 1.3 60.7 + - - +
123A THR 3.5 0.3 + - - -
124A MET* 3.7 16.0 + - - +
125A TYR* 5.2 0.3 + - - -
48B PRO* 4.3 23.1 - - - +
49B MET* 3.5 24.5 - - - +
62B PHE* 4.8 4.0 - - - -
228B TRP* 5.8 1.9 - - - -
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Residues in contact with ALA 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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99A HIS* 3.3 9.4 + - + +
103A PHE* 3.3 34.8 - - + -
118A GLN 2.9 18.9 + - - +
119A MET 4.3 1.8 - - - +
121A GLY* 1.3 78.2 - - - +
123A THR* 1.3 59.2 + - + +
125A TYR* 3.2 25.3 - - - -
49B MET* 3.7 4.9 - - + +
62B PHE* 3.7 25.2 - - + +
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Residues in contact with THR 123 (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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95A ILE* 5.1 0.7 - - + -
99A HIS* 3.7 5.2 - - + -
100A LEU* 3.7 23.3 - - + -
119A MET 2.7 22.5 + - - +
120A LEU* 3.6 3.6 + - - +
122A ALA* 1.3 76.7 - - - +
124A MET* 1.3 66.5 + - - +
125A TYR 3.1 3.4 - - - -
126A TYR* 2.9 35.5 + - + +
127A SER* 2.8 27.5 + - - -
133A VAL* 4.0 13.5 - - + -
137A ILE* 3.3 19.7 - - + +
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Residues in contact with MET 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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120A LEU* 3.1 22.2 + - + +
121A GLY* 3.7 11.7 - - - +
122A ALA 3.5 0.8 - - - -
123A THR* 1.3 78.7 - - - +
125A TYR* 1.3 60.8 + - - +
126A TYR 3.3 0.7 + - - -
127A SER* 3.8 15.3 + - - +
128A GLY* 4.7 2.8 + - - -
48B PRO* 3.7 32.8 - - + -
229B MET* 3.7 25.4 - - + +
256B PRO* 3.6 37.5 - - + -
257B PRO* 4.4 11.2 - - + +
258B GLN* 5.1 7.4 - - - +
281B HIS* 4.8 4.9 - - - +
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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