Contacts of the helix formed by residues 84 - 94 (chain D) in PDB entry 3JAX
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 CYS 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D GLY* 1.3 73.7 - - - +
85D PHE* 1.3 66.6 + - - +
86D GLU* 3.9 18.4 - - - +
87D ASP* 2.9 33.4 + - - -
88D TYR* 2.9 22.9 + - - -
148D LEU* 3.6 9.9 - - - -
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Residues in contact with PHE 85 (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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746B PHE* 6.0 1.3 - + - -
84D CYS* 1.3 74.5 - - - +
86D GLU* 1.3 80.4 + - + +
88D TYR 3.3 0.5 + - - -
89D VAL* 2.8 61.4 + - + +
141D GLU* 3.4 25.4 - - - -
144D VAL* 3.5 15.0 - - + -
145D ARG* 3.3 54.5 - - + -
148D LEU* 3.6 13.7 - - + +
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Residues in contact with GLU 86 (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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745B GLY* 4.2 16.0 - - - +
84D CYS* 3.3 15.5 - - - +
85D PHE* 1.3 103.4 + - + +
87D ASP* 1.3 67.3 + - - +
89D VAL* 3.2 22.9 - - + +
90D GLU* 3.6 9.2 + - - +
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Residues in contact with ASP 87 (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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795B VAL* 5.0 14.9 - - + +
82D GLN 4.7 0.5 - - - +
83D GLY* 3.3 9.3 - - - -
84D CYS* 2.9 39.3 + - - +
86D GLU* 1.3 77.6 - - - +
88D TYR* 1.3 68.1 + - + +
90D GLU* 3.4 12.5 + - - +
91D GLY* 2.9 23.6 + - - -
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Residues in contact with TYR 88 (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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795B VAL* 4.3 16.2 - - + +
798B ALA* 2.7 37.1 + - - +
799B PHE* 3.9 31.2 - + + -
802B GLN* 3.3 23.7 + - + -
82D GLN* 4.5 0.5 + - - -
83D GLY* 3.3 31.2 + - - -
84D CYS 2.9 27.3 + - - +
85D PHE 3.3 0.4 + - - -
87D ASP* 1.3 81.0 - - + +
89D VAL* 1.3 55.3 + - - +
90D GLU 3.3 0.4 - - - -
91D GLY* 4.1 4.5 - - - +
92D LEU* 2.7 36.3 + - + +
144D VAL* 3.2 23.5 - - + +
147D VAL* 4.6 4.3 - - + -
148D LEU* 3.6 17.5 - - + -
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Residues in contact with VAL 89 (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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745B GLY* 4.4 5.4 - - - +
746B PHE* 3.7 30.0 - - + -
85D PHE* 2.8 57.7 + - + +
86D GLU* 3.2 24.0 - - + +
88D TYR* 1.3 70.4 - - - +
90D GLU* 1.3 56.8 + - - +
93D ARG* 2.7 33.3 + - - +
140D TYR* 3.3 6.1 - - + -
141D GLU* 3.5 14.8 - - - +
144D VAL* 3.7 13.9 - - + -
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Residues in contact with GLU 90 (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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731B ARG* 4.5 5.2 - - - +
735B GLU* 3.4 40.0 - - - +
736B ILE* 3.5 21.1 - - - +
742B ILE* 3.9 28.4 - - + +
743B PRO* 5.2 2.1 - - - +
745B GLY 3.4 23.1 - - - +
746B PHE* 5.2 2.2 - - - +
747B MET* 6.0 0.2 - - + -
795B VAL* 5.4 0.2 - - - +
86D GLU 4.0 4.0 - - - +
87D ASP* 3.4 14.3 + - - +
88D TYR 3.3 0.2 - - - -
89D VAL* 1.3 78.6 - - - +
91D GLY* 1.3 75.3 + - - +
92D LEU 3.1 0.2 - - - -
93D ARG* 2.9 27.4 + - - +
94D VAL* 3.2 12.1 + - - +
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Residues in contact with GLY 91 (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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735B GLU* 4.6 0.7 - - - -
795B VAL* 4.9 6.5 - - - -
796B ILE* 3.6 19.0 - - - +
799B PHE* 4.8 4.2 - - - +
87D ASP 2.9 11.4 + - - -
88D TYR* 3.5 6.7 - - - -
90D GLU* 1.3 89.7 + - - +
92D LEU* 1.3 61.5 + - - +
94D VAL* 3.1 27.3 - - - +
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Residues in contact with LEU 92 (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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799B PHE* 3.6 42.4 - - + -
88D TYR* 2.7 21.8 + - + +
89D VAL 3.6 0.4 - - - -
91D GLY* 1.3 77.2 - - - +
93D ARG* 1.3 60.6 + - - +
94D VAL* 2.9 6.6 + - - +
95D PHE* 3.6 24.4 + - + -
103D VAL* 3.4 10.4 - - - +
140D TYR* 3.3 19.6 - - + +
143D LEU* 3.9 19.7 - - + +
144D VAL* 3.7 39.7 - - + +
147D VAL* 3.9 11.4 - - + -
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Residues in contact with ARG 93 (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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731B ARG* 4.3 6.9 - - - +
732B GLN* 2.8 27.5 + - - +
746B PHE* 3.6 29.3 - - - +
747B MET 4.5 13.3 + - - +
748B ASP* 6.3 0.2 - - - +
89D VAL 2.7 21.2 + - - +
90D GLU* 3.3 10.1 - - - +
92D LEU* 1.3 70.2 - - - +
94D VAL* 1.3 48.7 + - - +
95D PHE 2.6 16.8 + - - -
96D ASP* 2.8 52.5 + - - +
99D GLY* 2.9 28.6 + - - -
101D GLY* 3.7 5.7 - - - +
140D TYR* 2.6 38.6 + - + +
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Residues in contact with VAL 94 (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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732B GLN* 2.5 38.3 - - - +
733B ARG* 3.6 21.3 - - - +
735B GLU* 3.8 21.1 - - + +
796B ILE* 4.2 16.8 - - + -
799B PHE* 5.5 1.3 - - + -
90D GLU 3.2 11.0 + - - +
91D GLY* 3.1 28.9 - - - +
92D LEU* 3.7 2.0 - - - -
93D ARG* 1.3 66.4 - - - +
95D PHE* 1.3 90.9 + - + -
111D VAL* 5.3 1.1 - - + -
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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