Contacts of the strand formed by residues 124 - 130 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D ARG* 4.0 30.1 + - + +
119D LEU 3.7 0.2 - - - +
120D PHE* 3.5 6.8 - - - +
121D ARG 2.8 43.5 + - - +
122D GLU* 3.9 11.0 - - - +
123D GLY* 1.3 76.5 - - - +
125D VAL* 1.3 64.7 + - - +
126D TRP* 3.6 22.6 + - + +
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Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ARG* 3.5 4.8 - - - +
84D ILE* 2.9 52.4 + - + +
96D LEU* 5.5 3.4 - - + -
118D ALA* 4.4 14.4 - - + -
119D LEU 3.6 2.7 - - - +
120D PHE* 4.1 30.5 - - + -
123D GLY 5.1 2.7 - - - +
124D ASP* 1.3 80.2 - - - +
126D TRP* 1.3 64.7 + - - +
127D ILE* 4.6 3.6 - - + -
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Residues in contact with TRP 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D VAL* 3.7 45.5 - - + -
68D GLU* 4.3 14.6 - - + -
81D VAL* 3.7 32.8 - - + -
82D LYS 3.4 12.8 - - - -
83D ARG* 3.2 54.3 - - + -
118D ALA* 3.3 5.4 - - - -
119D LEU* 2.8 61.5 + - + +
121D ARG* 4.6 12.3 + - + +
124D ASP* 3.6 23.7 + - + +
125D VAL* 1.3 80.7 - - - +
127D ILE* 1.3 64.0 + - - +
128D CYS 3.7 0.2 + - - -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ALA 3.4 2.1 - - - +
81D VAL* 3.4 3.6 - - - -
82D LYS* 2.7 43.0 + - + +
84D ILE* 3.6 32.8 - - + -
96D LEU* 4.5 8.3 - - + -
100D LEU* 4.2 24.9 - - + -
115D PHE* 3.6 36.1 - - + -
117D GLY 3.6 5.4 - - - +
118D ALA* 4.4 7.0 - - + -
125D VAL* 4.6 2.7 - - + -
126D TRP* 1.3 77.4 - - - +
128D CYS* 1.3 64.0 + - - +
129D MSE 3.9 5.7 + - + +
200D ILE* 4.0 14.1 - - + -
204D LEU* 4.4 4.5 - - + -
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Residues in contact with CYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D VAL* 3.8 26.0 - - + -
53D LEU* 5.1 2.0 - - - -
79D MSE 4.0 22.0 - - + -
80D ALA 3.3 4.7 - - - +
81D VAL* 4.4 16.4 - - - -
115D PHE* 3.7 2.6 - - - -
116D TYR* 2.9 22.6 + - + -
117D GLY 2.6 28.8 + - - +
119D LEU* 4.0 24.5 - - - -
126D TRP 4.3 0.4 - - - -
127D ILE* 1.3 76.9 - - - +
129D MSE 1.3 64.3 + - - +
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Residues in contact with MSE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D MSE 3.5 4.4 - - - +
80D ALA* 2.8 54.2 + - + +
82D LYS* 4.4 18.6 - - - -
113D VAL* 3.9 17.3 - - + -
114D THR 3.5 7.2 - - - +
115D PHE* 3.7 39.5 - - + -
116D TYR* 3.3 10.6 - - - -
127D ILE* 4.5 7.9 - - + +
128D CYS* 1.3 78.0 - - - +
130D GLU* 1.3 66.8 + - - +
186D LEU* 4.1 19.1 - - + -
196D CYS* 4.2 6.3 - - - -
200D ILE* 4.4 4.7 - - + -
204D LEU* 4.8 12.3 - - - -
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ALA* 4.2 1.0 - - - +
112D THR 4.3 0.5 - - - +
113D VAL* 3.7 8.0 - - + +
114D THR* 2.8 44.5 + - - +
116D TYR* 3.3 25.4 - - + +
129D MSE 1.3 85.6 - - - +
131D LEU* 1.3 71.2 + - - +
132D MSE 3.3 24.8 + - + +
186D LEU* 5.2 0.9 - - - +
188D ASN* 5.3 0.3 + - - -
192D GLN* 5.0 1.9 - - - +
194D LYS* 2.6 35.4 + - - -
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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