Contacts of the strand formed by residues 124 - 130 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ARG* 2.3 39.8 + - - -
86A ALA* 4.0 7.4 + - - +
205A VAL* 4.2 8.3 - - - +
83C ARG* 3.5 19.8 + - - +
119C LEU 3.7 0.7 - - - +
120C PHE* 3.5 5.7 - - - +
121C ARG 2.7 39.1 + - - +
122C GLU* 3.9 6.4 - - - +
123C GLY* 1.3 85.5 - - - +
125C VAL* 1.3 64.4 + - - +
126C TRP* 3.3 21.5 - - + +
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ARG* 3.4 5.9 - - - +
84C ILE* 2.9 51.7 + - + +
93C GLN* 4.1 21.1 - - + +
97C LEU* 5.0 7.2 - - + -
118C ALA* 4.3 12.3 - - + -
119C LEU 3.4 6.3 - - - +
120C PHE* 3.5 36.3 - - + -
123C GLY 5.7 0.4 - - - +
124C ASP* 1.3 75.6 - - - +
126C TRP* 1.3 69.3 + - - +
127C ILE* 4.6 1.6 - - + -
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Residues in contact with TRP 126 (chain C).
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* 4.2 9.2 - - - -
205A VAL* 4.7 3.8 - - + -
206A ASP 5.9 0.2 - - - -
66C VAL* 3.8 38.4 - - + -
68C GLU* 4.3 9.4 - - + -
81C VAL* 3.8 39.7 - - + -
82C LYS 3.3 7.0 - - - -
83C ARG* 3.4 41.3 - - + -
118C ALA* 3.2 4.3 - - - +
119C LEU* 2.6 56.3 + - + +
121C ARG* 4.0 19.6 + - + +
124C ASP* 3.3 36.0 + - + +
125C VAL* 1.3 77.3 - - - +
127C ILE* 1.3 63.4 + - - +
128C CYS 4.1 0.2 + - - -
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ALA 3.6 1.6 - - - +
81C VAL* 3.4 2.8 - - - -
82C LYS* 2.7 39.3 + - + +
84C ILE* 3.5 34.8 - - + -
96C LEU* 4.3 7.6 - - + -
97C LEU* 5.1 0.4 - - + -
100C LEU* 4.0 28.0 - - + -
115C PHE* 3.9 33.0 - - + -
117C GLY 3.7 2.7 - - - +
118C ALA* 4.3 8.3 - - + -
125C VAL* 4.6 1.8 - - + -
126C TRP* 1.3 77.5 - - - +
128C CYS* 1.3 64.4 + - - +
129C MSE 4.0 6.6 + - - +
200C ILE* 4.2 9.9 - - + -
204C LEU* 3.9 10.8 - - + -
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Residues in contact with CYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS* 6.4 1.6 - - - -
50C ALA 6.3 0.7 - - - -
54C GLU* 4.8 4.0 - - - -
79C MSE 4.2 14.6 - - - -
80C ALA 3.2 6.3 - - - +
81C VAL* 3.9 15.7 - - - -
115C PHE* 3.7 1.9 - - - -
116C TYR* 2.9 39.8 + - + -
117C GLY 2.9 22.3 + - - +
119C LEU* 3.3 35.4 - - - -
127C ILE* 1.3 74.6 - - - +
129C MSE 1.3 63.5 + - - +
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Residues in contact with MSE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA* 5.3 1.1 - - + +
64A TYR* 4.1 26.5 - - + -
79C MSE 3.5 4.7 - - - +
80C ALA* 2.7 52.8 + - + +
82C LYS* 4.4 13.7 - - + -
113C VAL* 3.8 21.8 - - + -
114C THR 3.5 11.7 - - - +
115C PHE* 3.7 27.1 - - + -
116C TYR* 3.6 9.3 - - - -
127C ILE* 4.7 7.6 - - + +
128C CYS* 1.3 75.9 - - - +
130C GLU* 1.3 67.9 + - - +
131C LEU 3.2 0.3 + - - -
186C LEU* 3.8 19.5 - - + -
196C CYS* 4.5 2.9 - - - -
200C ILE* 5.0 0.9 - - + -
204C LEU* 4.7 8.5 - - - -
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Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ILE 5.3 1.1 - - - -
79C MSE 5.3 0.4 - - - +
80C ALA* 4.3 0.5 - - - +
112C THR 4.2 0.3 - - - +
113C VAL* 3.5 13.3 - - + +
114C THR* 2.8 49.4 + - - +
116C TYR* 3.5 13.5 - - - +
129C MSE 1.3 86.8 - - - +
131C LEU* 1.3 72.2 + - - +
132C MSE 3.5 20.6 + - + +
186C LEU* 5.0 0.5 - - - +
188C ASN* 5.5 0.2 + - - -
192C GLN* 5.1 1.4 - - - +
194C LYS* 2.7 34.6 + - - +
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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