Contacts of the helix formed by residues 114 - 126 (chain A) in PDB entry 1EGE
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ASN* 4.3 21.6 + - - +
113A ASN* 1.3 73.4 - - - +
115A GLN* 1.3 56.8 + - - +
117A LYS* 3.5 27.0 + - - +
118A LYS* 2.8 42.8 + - + +
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Residues in contact with GLN 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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113A ASN* 2.7 22.3 + - - +
114A ASP* 1.3 73.2 - - - +
116A GLN* 1.3 60.8 + - + +
118A LYS* 3.9 3.9 - - - +
119A LYS* 3.1 25.5 + - - +
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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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108A ILE* 5.0 5.6 - - + +
112A GLY* 3.4 20.1 - - - -
113A ASN* 2.7 37.3 + - - +
115A GLN* 1.3 74.8 - - + +
117A LYS* 1.3 58.5 + - + +
119A LYS* 3.3 4.5 + - - -
120A TYR* 2.8 46.6 + - + +
198A ILE* 4.3 15.9 - - + +
235A GLU 3.5 13.1 + - - +
236A ASN* 5.7 1.3 - - - +
237A VAL 2.8 28.6 + - - +
238A LEU* 4.0 19.9 + - - +
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Residues in contact with LYS 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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67A PRO* 5.2 14.7 - - - +
70A CYS* 3.6 15.9 - - - -
108A ILE* 4.2 13.2 - - + -
109A ILE* 4.4 21.3 + - - +
112A GLY* 2.8 36.1 + - - +
113A ASN 2.9 15.3 + - - +
114A ASP* 3.5 26.7 + - - +
116A GLN* 1.3 74.9 - - - +
118A LYS* 1.3 64.3 + - - +
121A LEU* 2.8 41.5 + - + +
122A GLY 3.3 0.5 + - - -
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Residues in contact with LYS 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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69A ASN* 2.7 60.0 + - - +
70A CYS* 3.7 9.5 - - - +
114A ASP* 2.8 32.7 + - + +
115A GLN* 3.9 4.7 - - - +
117A LYS* 1.3 71.2 - - - +
119A LYS* 1.3 59.8 + - - +
122A GLY* 2.8 29.2 + - - -
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Residues in contact with LYS 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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115A GLN 3.1 16.5 + - - +
116A GLN* 3.6 3.6 - - - +
118A LYS* 1.3 82.9 - - - +
120A TYR* 1.3 93.4 + - + +
123A ARG* 3.3 46.1 + - - +
200A GLU* 3.8 7.2 + - - -
236A ASN* 5.1 1.2 + - - +
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Residues in contact with TYR 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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108A ILE* 4.3 10.3 - - + -
116A GLN* 2.8 27.5 + - + +
119A LYS* 1.3 95.9 + - + +
121A LEU* 1.3 60.3 + - - +
123A ARG* 3.2 36.4 - - - +
124A MET* 3.0 21.2 - - - +
175A TRP* 3.3 25.3 + + + +
198A ILE* 3.6 35.0 - - + -
200A GLU* 3.3 35.7 + - + +
236A ASN* 3.0 37.0 + - - -
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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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66A ILE* 3.7 23.2 - - + +
67A PRO* 4.5 9.0 - - + -
70A CYS* 4.3 5.6 - - - -
105A GLN* 3.8 38.8 - - + +
108A ILE* 3.8 26.2 - - + -
109A ILE* 3.4 29.4 - - + -
117A LYS* 2.8 30.9 + - + +
120A TYR* 1.3 74.5 - - - +
122A GLY* 1.3 65.4 + - - +
124A MET* 3.1 18.8 - - + +
125A THR* 3.4 9.2 + - - -
175A TRP* 4.3 6.7 - - + -
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Residues in contact with GLY 122 (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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70A CYS* 4.3 17.0 - - - +
117A LYS 3.3 2.2 + - - -
118A LYS* 2.8 22.8 + - - -
121A LEU* 1.3 77.5 - - - +
123A ARG* 1.3 63.5 + - - +
125A THR* 2.8 21.5 + - - -
126A GLU* 3.4 15.4 + - - +
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Residues in contact with ARG 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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119A LYS* 3.3 32.2 + - - +
120A TYR* 3.2 41.3 - - - +
122A GLY* 1.3 73.9 - - - +
124A MET* 1.3 69.8 - - + +
125A THR 3.1 0.2 + - - -
126A GLU* 3.2 10.1 + - - +
127A GLU* 3.1 28.3 + - + +
129A LEU* 3.9 14.2 - - + +
174A ASN* 2.8 45.2 + - - +
175A TRP* 4.0 7.0 - - - -
200A GLU* 3.4 23.8 + - - +
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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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57A TRP* 3.3 14.6 + - - -
63A ASN* 3.9 15.1 - - - +
66A ILE* 3.8 13.0 - - + -
101A ASN* 4.4 4.9 - - - +
105A GLN* 3.6 24.7 - - - +
120A TYR 3.0 15.9 - - - +
121A LEU* 3.1 17.0 - - - +
122A GLY 3.0 0.2 + - - -
123A ARG* 1.3 79.4 - - + +
125A THR* 1.3 56.2 + - - +
127A GLU 3.1 16.5 - - - +
128A PRO* 4.4 0.9 - - - +
129A LEU* 3.5 47.4 + - + +
130A MET 4.8 3.4 - - - +
131A CYS* 4.0 6.1 - - - -
174A ASN* 4.6 2.2 - - + +
175A TRP* 3.2 39.9 - - + +
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Residues in contact with THR 125 (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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57A TRP* 3.2 25.0 + - - +
63A ASN* 6.3 0.2 - - - -
66A ILE* 3.9 13.8 - - - +
70A CYS 3.7 12.9 + - - +
71A GLY* 3.2 26.1 + - - +
72A GLY* 4.9 2.3 - - - -
73A LEU* 6.6 0.4 - - + -
121A LEU 3.4 12.6 + - - -
122A GLY 2.8 8.5 + - - -
124A MET* 1.3 78.2 - - - +
126A GLU* 1.3 60.1 + - + -
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Residues in contact with GLU 126 (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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57A TRP* 4.0 9.6 - - - -
122A GLY* 3.4 16.3 + - - +
123A ARG* 3.2 10.1 + - - +
125A THR* 1.3 78.4 - - - +
127A GLU* 1.3 80.4 + - + +
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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