Contacts of the strand formed by residues 78 - 83 (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 ILE 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ILE 5.4 3.8 - - - +
69C LYS* 4.4 18.6 - - + -
70C MSE 3.2 14.4 - - - +
71C ARG* 3.6 51.4 - - + +
76C GLY 4.5 3.4 - - - +
77C GLN* 1.3 82.0 + - - +
79C MSE 1.3 64.4 + - - +
116C TYR* 5.4 0.2 - - - -
130C GLU* 5.3 1.6 - - - -
131C LEU* 4.5 24.5 + - + +
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Residues in contact with MSE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 4.4 14.6 - - - +
69C LYS* 3.4 3.1 - - - +
70C MSE 2.7 36.4 + - - +
72C HIS* 3.9 33.4 - - + +
75C SER* 5.3 0.2 - - - +
77C GLN* 3.6 16.4 - - + +
78C ILE* 1.3 79.6 - - - +
80C ALA* 1.3 67.3 + - - +
81C VAL* 3.9 5.0 + - + +
116C TYR* 3.3 50.9 - - + -
128C CYS* 4.2 15.5 - - - -
129C MSE 3.5 10.1 - - - +
131C LEU* 4.6 5.6 - - - +
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY* 4.6 3.8 - - - -
63A ALA 5.4 0.9 - - - +
68C GLU 3.4 6.3 - - - +
79C MSE 1.3 73.5 - - - +
81C VAL* 1.3 62.4 + - - +
82C LYS* 3.9 20.0 - - - -
127C ILE 3.6 0.6 - - - +
128C CYS* 3.2 4.9 - - - -
129C MSE 2.7 52.7 + - + +
130C GLU 4.3 0.2 - - - +
131C LEU* 4.0 27.0 - - + +
132C MSE 5.4 0.2 - - - +
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Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 4.3 7.2 - - - +
66C VAL* 6.3 1.3 - - + -
68C GLU* 2.8 43.0 + - - +
70C MSE 4.1 28.0 - - + -
79C MSE 4.0 11.7 - - + +
80C ALA* 1.3 81.8 - - - +
82C LYS* 1.3 61.4 + - - +
119C LEU* 4.2 13.5 - - + -
126C TRP* 3.8 33.2 - - + -
127C ILE 3.4 2.7 - - - -
128C CYS* 3.9 17.7 - - + -
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Residues in contact with LYS 82 (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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61A ARG* 3.3 22.0 + - - +
62A GLY 3.5 1.7 + - - -
63A ALA 3.0 24.1 + - - +
64A TYR* 3.0 24.8 + - + +
65A GLY* 4.0 4.3 - - - +
68C GLU* 2.6 34.0 + - - +
80C ALA* 3.9 19.5 - - + -
81C VAL* 1.3 84.3 - - - +
83C ARG* 1.3 62.8 + - - +
84C ILE 3.7 0.3 + - - -
126C TRP* 3.6 5.4 - - - -
127C ILE* 2.7 40.8 + - + +
129C MSE 4.4 17.7 - - - -
204C LEU* 4.1 20.4 - - + +
205C VAL 5.9 0.2 - - - +
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Residues in contact with ARG 83 (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* 3.1 54.3 - - - +
124A ASP* 2.8 40.0 + - - -
126A TRP* 3.9 7.1 - - - -
68C GLU* 5.4 2.2 + - - +
82C LYS* 1.3 73.7 - - - +
84C ILE* 1.3 73.8 + - - +
86C ALA* 4.5 8.3 - - - +
124C ASP* 3.5 19.5 + - + -
125C VAL 3.4 12.6 - - - +
126C TRP* 3.4 22.4 - - + -
204C LEU* 3.5 6.2 - - - +
205C VAL* 3.0 60.0 + - + +
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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