Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 2ERY
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLY* 3.5 23.0 - - - +
23A GLY* 5.3 1.0 - - - -
99A GLY 3.0 14.8 + - - +
100A SER* 3.5 16.0 - - - +
101A PHE 3.2 0.4 - - - -
102A GLU* 1.3 73.9 - - - +
104A ILE* 1.3 64.3 + - - +
105A TYR 3.2 0.2 - - - -
106A LYS* 3.0 35.6 + - + +
107A PHE* 3.3 36.7 - - + -
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Residues in contact with ILE 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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91A LEU* 3.9 20.9 - - + -
92A VAL 3.7 31.0 - - - +
93A PHE* 4.0 9.2 - - + -
100A SER 3.7 8.5 - - - +
101A PHE 3.3 16.8 - - - +
102A GLU 3.1 1.0 - - - -
103A GLU* 1.3 77.2 - - - +
105A TYR* 1.3 63.2 + - - +
107A PHE* 3.1 15.3 + - + +
108A GLN* 3.1 19.9 + - - +
124A LEU* 3.7 28.0 - - + -
145A LEU* 4.0 8.1 - - + -
149A LEU* 3.6 26.5 - - + -
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Residues in contact with TYR 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 PHE* 4.8 5.5 - + - -
102A GLU* 3.3 48.7 + - - +
103A GLU 3.2 0.6 - - - -
104A ILE* 1.3 79.9 - - - +
106A LYS* 1.3 63.4 + - + +
108A GLN* 3.5 5.5 + - - +
109A ARG* 3.1 36.2 + - - +
145A LEU* 3.4 30.1 - - + +
148A GLN* 3.1 27.0 + - + -
149A LEU* 4.3 14.8 - - + -
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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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102A GLU 5.1 2.0 - - - +
103A GLU* 3.0 32.4 + - + +
105A TYR* 1.3 78.3 - - + +
107A PHE* 1.3 58.7 + - + +
109A ARG* 3.4 27.4 + - - +
110A GLN* 3.0 47.0 + - - +
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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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20A VAL* 4.0 30.1 - - + -
21A GLY* 3.5 46.7 - - - -
22A GLY* 3.9 3.8 - - - -
79A ARG* 6.4 2.0 - - - -
82A TYR* 6.2 0.2 - - - -
83A MET* 4.4 7.1 - - + +
91A LEU* 4.4 7.0 - - + -
100A SER 5.7 0.2 - - - -
103A GLU* 3.3 47.7 + - + -
104A ILE* 3.1 14.8 + - + +
106A LYS* 1.3 81.9 - - + +
108A GLN* 1.3 61.9 + - - +
110A GLN* 3.3 19.8 + - - +
111A ILE* 3.0 31.0 + - + +
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Residues in contact with GLN 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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91A LEU* 4.5 11.1 - - + +
104A ILE 3.1 14.3 + - - +
105A TYR 3.9 2.9 - - - +
107A PHE* 1.3 76.5 - - - +
109A ARG* 1.3 86.5 + - - +
111A ILE* 3.3 10.1 + - - +
112A LEU* 3.0 45.2 + - - +
122A MET* 3.9 22.4 - - + -
149A LEU* 3.8 51.1 + - + +
151A VAL* 6.0 0.2 - - + -
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Residues in contact with ARG 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 TYR* 3.1 25.7 + - - +
106A LYS* 3.7 33.0 - - - +
108A GLN* 1.3 88.1 + - - +
110A GLN* 1.3 62.7 + - - +
112A LEU* 3.5 5.2 + - - +
113A ARG* 3.0 33.6 + - - +
56B VAL* 6.0 5.6 - - + -
59B ASP* 3.7 29.5 + - - +
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Residues in contact with GLN 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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75A PHE* 3.3 50.2 - - + +
83A MET* 3.5 20.2 - - + +
106A LYS* 3.0 32.7 + - + +
107A PHE* 3.7 19.8 - - - +
109A ARG* 1.3 76.8 - - + +
111A ILE* 1.3 63.1 + - - +
113A ARG* 3.3 24.6 + - - +
114A VAL* 3.0 27.9 + - - +
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Residues in contact with ILE 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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20A VAL* 4.7 3.8 - - + -
83A MET* 3.8 29.4 - - + -
89A PHE* 3.7 48.0 - - + -
91A LEU* 3.8 23.3 - - + -
107A PHE 3.0 24.1 + - - +
108A GLN 3.7 3.4 - - - +
110A GLN* 1.3 75.5 - - - +
112A LEU* 1.3 58.4 + - - +
114A VAL* 3.2 4.5 + - - +
115A LYS* 2.9 43.5 + - + +
120A PHE* 4.5 2.7 - - + -
122A MET* 3.4 24.5 - - + -
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Residues in contact with LEU 112 (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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108A GLN* 3.0 45.3 + - + +
109A ARG* 4.1 4.7 - - - +
111A ILE* 1.3 76.4 - - - +
113A ARG* 1.3 58.0 + - - +
115A LYS* 4.5 1.8 - - + -
116A ASP* 2.8 24.8 + - - -
117A ARG* 3.3 25.7 + - + +
118A ASP* 3.7 20.6 - - - +
119A GLU* 3.9 24.5 - - - +
120A PHE* 3.9 7.4 - - + -
122A MET* 3.8 20.4 - - + -
169B HIS* 5.8 0.2 - - - -
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Residues in contact with ARG 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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75A PHE* 3.3 34.6 - - - -
80A GLU* 5.6 1.0 + - - -
109A ARG* 3.0 44.1 + - - +
110A GLN* 3.5 22.8 - - - +
111A ILE 3.2 0.2 - - - -
112A LEU* 1.3 72.3 - - - +
114A VAL* 1.3 67.6 + - + +
116A ASP* 3.3 13.7 + - - +
58B ASP* 5.0 11.4 - - - +
59B ASP* 3.0 47.1 + - - +
173B ARG* 5.5 2.3 + - - -
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Residues in contact with VAL 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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75A PHE* 4.4 3.1 - - + -
80A GLU* 3.6 53.6 - - + +
83A MET* 4.0 14.6 - - + +
84A ARG* 3.6 46.4 + - + +
110A GLN 3.0 20.6 + - - +
111A ILE 3.7 3.6 - - - +
113A ARG* 1.3 80.8 - - + +
115A LYS* 1.3 61.9 + - - +
116A ASP* 3.4 2.1 + - - +
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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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83A MET 2.9 24.9 + - - +
84A ARG* 3.0 19.1 + - - +
85A THR 4.4 0.2 - - - -
86A GLY 2.7 24.8 + - - -
89A PHE* 4.1 5.4 - - - -
111A ILE* 2.9 23.6 + - + +
112A LEU* 4.0 4.7 - - - +
114A VAL* 1.3 77.7 - - + +
116A ASP* 1.3 70.0 + - - +
117A ARG* 3.3 20.9 + - + +
120A PHE* 3.4 44.5 - - + -
166B GLN* 3.6 16.3 + - - -
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Residues in contact with ASP 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 LEU 2.8 10.7 + - - -
113A ARG* 3.3 7.9 + - - +
114A VAL 3.3 5.2 - - - +
115A LYS* 1.3 78.1 - - - +
117A ARG* 1.3 57.1 - - - +
57B ILE* 5.8 0.2 - - - -
154B MET* 5.9 0.3 - - - +
166B GLN* 3.4 42.8 + - + +
169B HIS* 2.7 36.0 + - - -
170B GLU* 4.8 0.9 - - - +
173B ARG* 2.9 40.3 + - - -
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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