Contacts of the strand formed by residues 78 - 83 (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 ILE 78 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PRO 4.4 15.0 - - - +
75C SER* 4.0 29.6 - - - +
56D ILE* 4.6 10.5 - - + -
69D LYS* 4.6 19.7 - - + -
70D MSE 3.5 4.0 - - - +
71D ARG* 4.2 35.9 - - + +
76D GLY 3.7 5.6 + - - +
77D GLN* 1.3 96.4 + - - +
79D MSE 1.3 67.8 + - - +
116D TYR* 4.7 1.4 + - - -
131D LEU* 4.5 18.6 + - + +
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Residues in contact with MSE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D VAL* 4.9 4.7 - - + -
53D LEU* 4.2 23.6 - - + -
69D LYS* 3.5 5.2 - - - -
70D MSE 2.8 50.2 + - - +
72D HIS* 4.2 23.1 - - + +
75D SER* 5.4 0.2 - - - +
77D GLN* 4.3 12.1 - - + +
78D ILE* 1.3 75.9 - - - +
80D ALA* 1.3 67.0 + - - +
81D VAL* 4.0 5.7 + - + +
116D TYR* 3.1 51.8 - - + -
128D CYS* 4.0 19.1 - - - -
129D MSE 3.5 12.3 - - - +
131D LEU* 4.4 8.4 - - - +
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Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D GLU 3.3 5.4 - - - +
79D MSE 1.3 74.1 - - - +
81D VAL* 1.3 60.6 + - - +
82D LYS* 3.8 19.5 - - - -
127D ILE 3.4 1.7 - - - +
128D CYS* 3.3 4.3 - - - -
129D MSE 2.8 51.9 + - + +
130D GLU 4.2 0.7 - - - +
131D LEU* 3.9 26.5 - - + +
132D MSE 5.4 0.9 - - - +
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LEU* 5.2 2.9 - - + -
66D VAL* 5.8 2.5 - - + -
67D VAL 5.1 0.4 - - - +
68D GLU* 2.8 41.9 + - - +
70D MSE 3.8 36.8 - - + -
79D MSE 4.2 9.4 - - + +
80D ALA* 1.3 78.9 - - - +
82D LYS* 1.3 65.1 + - - +
119D LEU* 4.1 17.7 - - + -
126D TRP* 3.7 32.9 - - + -
127D ILE 3.4 2.7 - - - -
128D CYS* 4.4 15.7 - - - -
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Residues in contact with LYS 82 (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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68D GLU* 3.1 33.6 + - - +
80D ALA* 3.8 23.0 - - - +
81D VAL* 1.3 87.9 - - - +
83D ARG* 1.3 63.6 + - - +
84D ILE 3.6 0.7 + - - -
126D TRP* 3.5 4.3 - - - -
127D ILE* 2.7 44.7 + - + +
129D MSE 4.4 18.8 - - - -
131D LEU* 6.2 0.4 - - - +
204D LEU* 4.1 27.0 - - + +
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Residues in contact with ARG 83 (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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68D GLU* 5.2 2.1 + - - +
82D LYS* 1.3 71.7 - - - +
84D ILE* 1.3 70.3 + - - +
86D ALA* 4.5 21.2 - - - +
124D ASP* 4.0 27.8 + - + +
125D VAL 3.5 11.7 - - - +
126D TRP* 3.2 43.6 - - + -
204D LEU* 3.6 5.9 - - - +
205D VAL* 3.0 67.9 + - + +
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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