Contacts of the strand formed by residues 73 - 78 (chain D) in PDB entry 2J0Q
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 TRP 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B ASP* 3.6 7.1 + - - -
45B LEU 5.7 1.3 - - - -
47B GLU* 5.1 9.4 - - + -
50B LEU* 3.6 28.9 - - + -
66D PRO* 3.7 39.0 - - + -
67D GLN* 3.8 4.0 - - - -
68D ARG* 3.4 55.1 - - + +
69D SER* 4.4 1.3 - - - +
72D GLY* 1.3 76.0 - - - -
74D ILE* 1.3 61.8 + - - +
75D LEU* 4.2 0.3 + - - +
119D VAL 3.7 1.0 - - - +
120D GLU* 3.2 1.6 - - - -
121D TYR* 2.8 39.5 + - - +
122D GLU 3.4 19.5 + - - -
123D THR 3.5 1.8 - - - -
124D TYR* 3.4 42.1 - + - +
127D ALA* 4.2 20.5 - - + +
148D TRP* 4.6 6.1 - + + -
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Residues in contact with ILE 74 (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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139C LEU* 3.2 35.2 - - + +
67D GLN 5.7 1.2 + - - -
69D SER* 2.9 30.5 + - - +
73D TRP* 1.3 73.1 - - - +
75D LEU* 1.3 77.3 + - - +
118D LEU* 3.7 20.6 - - + -
119D VAL 3.3 6.7 - - - +
120D GLU* 3.6 22.7 - - + +
148D TRP* 3.9 7.6 - - - -
149D CYS* 3.0 38.5 + - + +
150D PHE* 3.7 16.4 + - + -
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Residues in contact with LEU 75 (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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74D ILE* 1.3 79.6 - - - +
76D PHE* 1.3 60.7 + - - +
77D VAL* 4.6 2.9 - - + +
93D PHE* 4.6 5.2 - - + -
117D THR 4.1 0.2 - - - +
118D LEU* 3.4 5.9 - - - -
119D VAL* 2.7 43.2 + - + +
121D TYR* 4.0 22.7 - - + -
127D ALA* 3.7 22.9 - - + +
130D ALA* 4.1 6.7 - - + -
131D MET* 4.2 10.8 - - - +
146D VAL* 3.7 24.5 - - + -
147D ASP 3.3 15.9 - - - +
148D TRP* 3.5 36.8 - - + -
149D CYS* 4.2 0.2 - - - -
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Residues in contact with PHE 76 (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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55C SER* 3.5 28.3 - - - +
56C VAL* 3.7 27.8 - - + -
59C GLU* 3.6 23.3 - - + -
132C LEU* 4.5 13.5 - - + -
136C LEU* 5.2 1.8 - - + -
75D LEU* 1.3 73.9 - - - +
77D VAL* 1.3 62.0 + - - +
78D THR* 3.4 27.3 + - + -
116D TYR* 3.9 29.2 - + + -
117D THR 4.0 0.7 - - - -
118D LEU* 4.1 22.4 - - + -
145D SER 3.7 0.9 - - - +
146D VAL* 3.5 3.8 - - - -
147D ASP* 2.9 34.1 + - - +
148D TRP 4.3 2.7 - - - +
149D CYS* 4.1 16.7 - - + +
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Residues in contact with VAL 77 (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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75D LEU* 4.6 5.6 - - + +
76D PHE* 1.3 81.8 - - - +
78D THR* 1.3 65.9 + - - +
80D VAL* 3.6 9.5 - - + +
93D PHE* 3.7 29.2 - - + -
116D TYR* 3.2 7.7 - - - -
117D THR* 2.9 53.9 + - + +
119D VAL* 4.7 5.2 - - + -
144D ILE* 4.2 20.6 - - + -
145D SER 3.2 15.3 - - - +
146D VAL* 4.1 8.5 - - + -
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Residues in contact with THR 78 (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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55C SER* 4.3 7.7 - - - +
59C GLU* 3.6 29.4 - - + +
76D PHE* 3.4 32.6 + - + -
77D VAL* 1.3 74.1 - - - +
79D GLY* 1.3 63.7 - - - +
80D VAL* 3.6 0.9 - - - -
115D GLY 3.8 4.5 - - - -
116D TYR* 4.8 0.2 - - + -
144D ILE* 3.4 4.2 - - - +
145D SER* 2.9 47.7 + - - +
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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