Contacts of the strand formed by residues 124 - 129 (chain A) in PDB entry 3ENM
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 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ARG* 3.9 11.9 + - + -
120A PHE* 3.6 6.9 - - - +
121A ARG 2.5 41.4 + - - +
122A GLU* 4.1 8.2 - - - +
123A GLY* 1.3 75.6 - - - +
125A VAL* 1.3 68.3 + - - +
126A TRP* 3.5 19.6 + - + +
83C ARG* 2.8 44.9 + - - -
86C ALA* 4.0 12.4 + - - +
205C VAL* 4.5 7.8 - - - +
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Residues in contact with VAL 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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83A ARG* 3.5 4.8 - - - +
84A ILE* 3.0 57.5 + - + +
118A ALA* 4.5 13.0 - - + -
119A LEU 3.6 3.4 - - - +
120A PHE* 3.9 29.4 - - + -
123A GLY 5.2 2.7 - - - +
124A ASP* 1.3 79.8 - - - +
126A TRP* 1.3 64.7 + - - +
127A ILE* 4.6 0.4 - - + -
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Residues in contact with TRP 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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66A VAL* 3.5 43.7 - - + -
68A GLU* 4.5 10.5 - - + -
81A VAL* 3.7 38.4 - - + -
82A LYS* 3.1 7.0 - - - -
83A ARG* 3.3 51.6 - - + -
118A ALA* 3.1 5.9 - - - +
119A LEU* 2.7 59.3 + - + +
121A ARG* 4.3 13.3 - - + +
124A ASP* 3.5 21.8 + - + +
125A VAL* 1.3 77.0 - - - +
127A ILE* 1.3 63.1 + - - +
128A CYS 3.9 0.2 + - - -
83C ARG* 3.9 12.6 - - - -
205C VAL* 4.9 1.6 - - + -
208C VAL* 4.3 11.8 - - + +
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Residues in contact with ILE 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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80A ALA 3.5 1.4 - - - +
81A VAL* 3.3 3.3 - - - -
82A LYS* 2.7 39.6 + - + +
84A ILE* 3.4 35.0 - - + -
96A LEU* 4.7 8.5 - - + -
100A LEU* 4.0 29.4 - - + -
115A PHE* 3.8 33.0 - - + -
117A GLY 3.6 4.7 - - - +
118A ALA* 4.4 8.3 - - + -
125A VAL* 4.6 0.7 - - + -
126A TRP* 1.3 76.8 - - - +
128A CYS* 1.3 63.9 + - - +
129A MSE 4.7 7.8 - - + +
200A ILE* 4.2 16.6 - - + -
204A LEU* 4.4 5.8 - - + -
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Residues in contact with CYS 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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48A VAL* 4.0 24.9 - - + -
53A LEU* 4.6 4.0 - - - -
79A MSE 4.0 20.2 - - + -
80A ALA 3.2 6.3 - - - +
81A VAL* 4.3 16.4 - - - -
115A PHE* 3.7 1.9 - - - -
116A TYR* 2.8 30.9 + - + -
117A GLY 2.9 16.6 + - - +
119A LEU* 4.1 22.9 - - - -
126A TRP 4.3 0.4 - - - -
127A ILE* 1.3 78.1 - - - +
129A MSE 1.3 63.2 + - - +
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Residues in contact with MSE 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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79A MSE 3.6 3.8 - - - +
80A ALA* 2.8 46.7 + - + +
82A LYS* 4.4 18.8 - - - -
113A VAL* 3.9 17.3 - - + -
114A THR 3.5 7.0 - - - +
115A PHE* 3.7 38.1 - - + -
116A TYR* 3.7 11.3 - - - -
127A ILE* 4.7 8.3 - - - +
128A CYS* 1.3 77.4 - - - +
130A GLU* 1.3 69.4 + - - +
186A LEU* 4.1 17.9 - - + -
196A CYS* 4.3 2.2 - - - -
200A ILE* 4.6 0.9 - - + -
204A LEU* 4.8 6.3 - - - -
63C ALA* 5.6 1.8 - - + +
64C TYR* 4.2 22.0 - - + -
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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