Contacts of the helix formed by residues 110 - 122 (chain A) in PDB entry 1ESD
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 PHE 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLY* 3.0 20.4 + - - +
106A ASN* 6.0 0.2 - - - +
108A LEU* 3.8 21.0 - - + -
109A GLY* 1.3 75.7 - - - +
111A ASN* 1.3 60.9 + - - +
113A ILE* 3.2 10.3 + - + +
114A LEU* 3.1 47.0 + - + +
189A LEU* 3.7 30.7 - - + -
220A LEU* 4.0 36.3 - - + -
223A ILE* 3.9 20.4 - - + -
224A GLN* 4.5 14.8 - - + -
227A LEU* 5.1 3.8 - - + -
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Residues in contact with ASN 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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106A ASN* 3.9 20.6 + - - +
109A GLY* 3.5 15.6 - - - -
110A PHE* 1.3 71.1 + - - +
112A ARG* 1.3 67.3 + - - +
114A LEU* 3.2 7.5 + - - +
115A LYS* 3.1 32.1 + - - +
127A LEU* 4.0 23.5 - - + +
128A PRO* 2.4 46.7 + - + +
129A GLY* 3.1 12.3 - - - -
400A VXA 5.9 1.8 - - - +
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Residues in contact with ARG 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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106A ASN 5.9 0.2 - - - -
109A GLY* 3.0 15.4 + - - +
111A ASN* 1.3 95.7 - - - +
113A ILE* 1.3 55.9 + - - +
114A LEU 3.3 0.2 - - - -
115A LYS* 4.7 1.1 - - - +
116A GLN* 3.1 27.2 + - - +
129A GLY* 4.4 1.8 - - - -
130A ASP* 3.1 35.1 + - - +
131A PRO* 3.1 23.6 + - - +
132A VAL* 3.6 29.7 + - + +
153A TRP* 3.6 32.3 - - + +
157A GLN* 4.8 4.5 + - - -
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Residues in contact with ILE 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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108A LEU* 4.3 7.4 - - + -
109A GLY 3.5 15.0 - - - +
110A PHE* 3.2 21.7 + - + +
112A ARG* 1.3 73.9 - - - +
114A LEU* 1.3 65.6 + - - +
116A GLN* 3.9 0.7 - - - +
117A CYS* 3.3 24.3 + - - -
145A PHE* 3.7 32.3 - - + -
153A TRP* 3.9 21.1 - - + -
154A LEU* 4.2 8.3 - - + -
220A LEU* 3.4 30.3 - - + +
223A ILE* 4.0 30.7 - - + -
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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
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110A PHE* 3.1 41.9 + - + +
111A ASN* 3.6 7.9 - - - +
113A ILE* 1.3 76.3 - - - +
115A LYS* 1.3 63.9 + - - +
117A CYS* 2.9 15.6 + - - +
118A SER* 3.0 13.7 + - - -
121A LEU* 4.0 14.1 - - + -
127A LEU* 4.4 14.6 - - + -
189A LEU* 5.8 0.2 - - + -
209A PHE* 5.0 8.5 - - + -
212A ILE* 4.1 13.0 - - + +
220A LEU* 4.2 20.6 - - + -
265A LEU* 3.8 23.3 - - + -
281A TYR 4.5 2.2 - - - +
282A ALA* 4.2 15.9 - - + -
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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 ASN 3.1 14.6 + - - +
112A ARG 4.3 0.4 - - - +
114A LEU* 1.3 74.4 - - - +
116A GLN* 1.3 61.5 + - - +
118A SER 3.1 16.6 - - - +
121A LEU* 3.6 29.7 + - + +
122A ARG* 3.1 23.4 + - - +
123A LYS 5.6 0.8 + - - -
125A SER* 3.8 15.2 + - - -
127A LEU* 2.5 40.5 + - + -
128A PRO 3.8 8.9 - - - -
129A GLY 2.6 32.7 + - - +
130A ASP* 4.5 3.4 - - - +
131A PRO* 4.2 20.9 - - + -
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Residues in contact with GLN 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 ARG 3.1 21.9 + - - +
113A ILE 3.9 1.3 - - - +
114A LEU 3.1 0.4 + - - -
115A LYS* 1.3 75.0 - - - +
117A CYS* 1.3 59.8 + - - +
122A ARG* 2.7 39.9 + - - +
131A PRO* 3.2 6.2 - - - +
132A VAL 2.9 23.1 + - - +
133A ASP* 2.8 34.8 + - - +
136A GLU* 3.4 19.6 - - - +
137A PRO 5.1 1.6 + - - -
138A ALA* 3.2 10.6 - - - +
141A CYS* 4.3 8.6 - - + +
144A PHE* 4.3 12.9 - - + +
145A PHE* 3.8 28.7 - - + -
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Residues in contact with CYS 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 ILE 3.3 14.3 + - - +
114A LEU* 2.9 8.6 + - - +
116A GLN* 1.3 76.0 - - - +
118A SER* 1.3 61.1 + - - -
138A ALA* 3.8 7.9 - - - +
141A CYS* 2.1 50.7 - - - -
145A PHE* 4.3 9.2 - - - -
211A ASP 3.9 1.6 - - - +
212A ILE* 3.3 28.7 - - + +
213A PRO* 3.4 15.0 - - + +
216A ALA* 4.5 2.2 - - - -
220A LEU* 5.0 10.1 - - + -
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Residues in contact with SER 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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114A LEU 3.0 11.0 + - - -
115A LYS 3.1 9.4 + - - +
116A GLN 3.2 1.2 + - - -
117A CYS* 1.3 83.1 - - - +
119A ASP* 1.3 53.8 + - - +
120A GLU* 3.6 0.7 - - - +
121A LEU* 3.0 23.4 + - - +
122A ARG* 2.8 33.6 + - - +
138A ALA* 4.0 1.6 - - - -
211A ASP* 2.6 28.2 + - - -
212A ILE* 3.3 18.8 - - - -
265A LEU* 4.5 3.0 - - - +
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Residues in contact with ASP 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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118A SER* 1.3 68.4 - - - +
120A GLU* 1.3 65.9 + - - +
121A LEU 3.0 1.8 - - - -
122A ARG* 3.1 31.3 + - + +
123A LYS* 3.5 12.5 - - - +
137A PRO* 5.1 1.9 - - - +
138A ALA* 3.0 30.3 + - - +
211A ASP* 3.8 10.0 + - - +
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Residues in contact with GLU 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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118A SER* 3.6 0.4 - - - +
119A ASP* 1.3 77.7 - - - +
121A LEU* 1.4 63.8 + - + +
123A LYS* 3.2 47.3 + - + +
124A PRO 5.5 0.2 - - - +
125A SER* 5.9 0.3 - - - -
206A GLN* 4.0 16.9 + - - -
211A ASP* 2.9 33.6 + - - +
266A LEU* 3.4 34.2 - - + +
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Residues in contact with LEU 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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114A LEU* 4.0 22.7 - - + -
115A LYS* 3.6 28.6 - - + +
118A SER* 3.0 20.0 + - - +
120A GLU* 1.4 81.2 - - - +
122A ARG* 1.3 58.1 - - - +
123A LYS 3.1 15.7 - - - +
125A SER* 3.9 10.9 + - - +
127A LEU* 4.2 15.5 - - + -
265A LEU* 3.5 39.7 - - + -
266A LEU* 4.2 25.4 - - + -
281A TYR* 4.4 18.4 - - + -
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Residues in contact with ARG 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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115A LYS* 3.1 23.0 + - - +
116A GLN* 2.7 46.6 + - - +
118A SER 2.8 18.3 + - - +
119A ASP* 3.1 27.7 + - + +
121A LEU* 1.3 76.9 - - - +
123A LYS* 1.3 56.0 + - - +
124A PRO* 4.8 0.3 - - - +
131A PRO* 3.9 19.9 - - + +
134A GLY* 3.2 27.1 + - - -
136A GLU 2.8 23.4 + - - -
137A PRO* 4.6 0.6 - - - +
138A ALA* 3.2 15.0 - - - +
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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