Contacts of the helix formed by residues 124 - 133 (chain A) in PDB entry 5EN1
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASP 4.2 7.9 - - - +
123A THR* 1.3 80.6 - - - +
125A GLU* 1.3 60.8 + - - +
126A HIS* 3.2 21.0 + - + +
127A HIS* 2.9 36.4 + - + +
128A LEU* 3.4 6.4 + - - +
143A ILE* 4.0 12.1 - - + +
152A LYS* 4.4 20.9 + - - -
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Residues in contact with GLU 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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124A GLU* 1.3 74.3 - - - +
126A HIS* 1.3 58.3 + - - +
128A LEU* 3.3 3.8 + - - +
129A ARG* 2.9 28.3 + - + +
141A ILE* 3.8 47.3 + - + +
143A ILE* 3.6 18.3 + - + +
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Residues in contact with HIS 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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124A GLU* 3.1 22.0 + - + +
125A GLU* 1.3 75.8 - - - +
127A HIS* 1.3 101.8 + + - +
129A ARG* 3.7 21.7 + - - +
130A ASP* 3.0 34.6 + - + +
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Residues in contact with HIS 127 (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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122A ASP 3.7 10.5 - - - -
123A THR* 3.8 12.1 - - + -
124A GLU* 2.9 28.9 + - + +
126A HIS* 1.3 111.3 + + - +
128A LEU* 1.3 60.2 + - - +
130A ASP* 4.0 3.6 - - - +
131A TYR* 3.0 30.1 + - - +
177A ILE* 4.5 6.0 - - + +
178A ASN* 3.4 44.0 + - + +
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Residues in contact with LEU 128 (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 VAL* 4.5 13.9 - - + -
119A ILE* 4.7 7.4 - - + -
123A THR* 4.3 9.6 - - + -
124A GLU 3.4 8.7 + - - +
125A GLU 3.3 7.0 + - - +
127A HIS* 1.3 74.9 - - - +
129A ARG* 1.3 55.8 + - - +
131A TYR* 3.2 2.1 + - - +
132A PHE* 2.8 47.1 + - + +
141A ILE* 3.8 22.0 - - + -
143A ILE* 3.8 24.5 - - + -
156A GLY* 5.1 7.9 - - - -
157A PHE 5.2 0.4 - - - +
158A VAL* 4.0 19.3 - - + -
177A ILE* 4.0 32.5 - - + -
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Residues in contact with ARG 129 (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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125A GLU* 2.9 21.9 + - + +
126A HIS* 3.7 31.3 + - - +
128A LEU* 1.3 70.9 - - - +
130A ASP* 1.3 92.0 + - - +
133A GLU* 2.8 70.0 + - + +
138A ILE* 4.0 8.1 - - + -
141A ILE* 3.6 21.4 - - + +
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Residues in contact with ASP 130 (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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126A HIS* 3.0 22.9 + - + +
127A HIS* 4.0 4.6 - - - +
129A ARG* 1.3 102.5 + - - +
131A TYR* 1.3 64.1 + - - +
133A GLU* 4.0 13.9 - - - +
134A GLU* 4.8 3.5 + - - +
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Residues in contact with TYR 131 (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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127A HIS 3.0 20.0 + - - +
128A LEU* 3.7 4.5 - - - +
130A ASP* 1.3 79.8 + - - +
132A PHE* 1.3 97.2 + + + +
134A GLU* 3.1 34.2 - - - +
135A TYR* 4.0 14.0 + + - -
174A TYR 4.8 0.3 + - - -
175A HIS* 2.8 40.4 + - + +
176A THR 3.5 24.8 + - - -
177A ILE* 4.0 18.6 - - + -
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Residues in contact with PHE 132 (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* 3.6 20.6 - - + -
116A VAL* 4.1 11.7 - - + -
128A LEU* 2.8 33.4 + - + +
131A TYR* 1.3 96.2 - + - +
133A GLU* 1.3 65.2 + - - +
134A GLU 3.1 2.7 - - - -
135A TYR* 2.9 27.5 + + - +
136A GLY 3.7 2.6 + - - -
138A ILE* 4.1 13.7 - - + -
158A VAL* 3.9 16.6 - - + -
160A PHE* 3.9 13.4 - + + -
169A ILE* 3.6 39.7 - - + -
175A HIS* 4.7 0.9 - - - -
177A ILE* 3.8 24.7 - - + -
184A VAL* 4.2 11.7 - - + -
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Residues in contact with GLU 133 (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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129A ARG* 2.8 70.1 + - + +
130A ASP* 4.0 11.6 - - - +
132A PHE* 1.3 69.7 - - - +
134A GLU* 1.3 58.1 + - - +
135A TYR 3.1 3.1 + - - -
136A GLY* 3.1 26.0 + - - +
138A ILE* 3.7 8.0 - - + +
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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