Contacts of the helix formed by residues 70 - 81 (chain D) in PDB entry 2J3W
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 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D HIS* 1.3 96.9 - - - +
71D PHE* 1.3 62.5 + - - +
72D ARG* 2.9 23.9 + - + +
73D GLU* 2.8 35.3 + - - +
74D THR* 3.4 17.5 + - - -
144D MET* 4.5 4.0 - - - +
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Residues in contact with PHE 71 (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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70D ASP* 1.3 76.0 - - - +
72D ARG* 1.3 65.7 + - + +
74D THR* 3.3 15.1 + - + -
75D ALA* 3.4 10.7 + - - +
96D TRP* 4.2 2.7 - + - -
100D GLY 3.5 23.6 - - - +
101D ASP 3.5 18.6 - - - -
102D GLU* 4.1 2.0 - - - -
103D PHE* 3.5 39.5 - + - -
139D LEU* 5.4 4.9 - - + -
144D MET* 4.1 14.3 - - - +
146D VAL* 4.0 15.3 - - + -
165D MET* 4.5 6.3 - - + -
166D ARG 4.3 3.6 - - - -
167D PHE* 3.5 53.2 - + + -
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Residues in contact with ARG 72 (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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70D ASP* 2.9 16.1 + - + +
71D PHE* 1.3 78.9 - - + +
73D GLU* 1.3 59.2 + - - +
75D ALA* 3.4 13.7 - - - +
76D ASP* 3.2 15.6 - - - +
96D TRP* 3.3 70.3 - - + +
97D SER 4.8 1.6 + - - -
100D GLY* 3.5 22.1 - - - +
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Residues in contact with GLU 73 (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 CYS* 4.9 5.8 - - - -
69D HIS* 2.9 53.1 + - + +
70D ASP* 2.8 23.9 + - - +
72D ARG* 1.3 71.3 - - - +
74D THR* 1.3 65.1 + - - +
75D ALA 3.2 0.4 - - - -
76D ASP* 3.4 13.2 + - + +
77D VAL* 3.2 26.4 + - + +
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Residues in contact with THR 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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68D CYS* 4.0 15.9 - - - +
70D ASP 3.4 13.9 + - - -
71D PHE* 3.3 12.6 + - + -
73D GLU* 1.3 75.6 - - - +
75D ALA* 1.3 66.0 + - - +
77D VAL* 3.3 8.5 + - - +
78D ILE* 3.0 29.1 + - + +
139D LEU* 3.7 30.7 - - + -
144D MET* 4.1 18.8 - - - +
1068D PLM 3.7 18.7 + - + -
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Residues in contact with ALA 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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71D PHE 3.4 4.7 + - - +
72D ARG 3.4 11.7 - - - +
73D GLU 3.2 0.2 - - - -
74D THR* 1.3 78.6 - - - +
76D ASP* 1.3 64.3 + - - +
78D ILE* 3.1 13.7 + - - +
79D ALA* 3.1 12.8 + - - +
93D ILE* 3.4 21.1 - - + +
96D TRP* 4.0 8.3 - - + -
103D PHE* 3.5 45.0 - - + -
105D LEU* 5.3 0.2 - - - +
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Residues in contact with ASP 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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72D ARG 3.2 16.8 - - - +
73D GLU* 3.4 14.1 + - + +
74D THR 3.3 0.6 - - - -
75D ALA* 1.3 78.9 - - - +
77D VAL* 1.3 57.8 + - + +
80D LYS* 2.8 69.9 + - + +
81D VAL* 5.1 0.2 - - - -
93D ILE* 3.5 14.0 - - - +
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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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59D PHE* 3.7 31.9 - - + -
63D SER* 6.2 0.2 - - - +
68D CYS* 4.0 19.5 - - - -
73D GLU* 3.2 20.9 - - + +
74D THR* 3.3 7.4 + - - +
75D ALA 3.3 0.4 - - - -
76D ASP* 1.3 75.1 - - + +
78D ILE* 1.3 58.9 + - - +
81D VAL* 2.8 45.7 + - + +
82D ALA 2.8 4.9 + - - -
1068D PLM 4.3 13.7 - - + -
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Residues in contact with ILE 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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74D THR* 3.0 31.4 + - + +
75D ALA* 3.1 10.5 + - - +
77D VAL* 1.3 78.1 - - - +
79D ALA* 1.3 61.7 + - - +
82D ALA* 3.3 8.5 + - - +
83D PHE* 2.9 56.3 + - + -
103D PHE* 4.7 5.8 - - + -
105D LEU* 4.3 9.9 - - + -
135D LEU* 3.8 16.6 - - + -
139D LEU* 4.2 21.5 - - + -
165D MET* 4.5 7.2 - - + -
1068D PLM 3.7 26.5 - - + -
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Residues in contact with ALA 79 (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 ALA 3.1 4.6 + - - +
78D ILE* 1.3 82.1 - - - +
80D LYS* 1.3 63.4 + - + +
81D VAL 3.7 0.2 + - - -
83D PHE* 3.8 4.3 - - - +
89D ILE 3.6 4.9 - - - +
90D THR* 3.4 9.6 - - - -
91D PRO* 3.1 49.1 - - + +
93D ILE* 3.9 15.3 - - + -
105D LEU* 3.6 25.1 - - + -
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Residues in contact with LYS 80 (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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76D ASP* 2.8 57.4 + - + +
79D ALA* 1.3 78.1 - - + +
81D VAL* 1.3 63.1 + - + +
84D LYS* 4.0 16.5 - - - +
90D THR* 4.1 19.7 + - + +
91D PRO 5.5 1.9 + - - +
93D ILE* 5.0 6.0 - - + +
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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
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59D PHE* 3.6 23.8 - - + -
63D SER* 4.6 12.8 - - - +
76D ASP 5.1 0.2 - - - -
77D VAL* 2.8 35.8 + - + +
80D LYS* 1.3 80.9 - - + +
82D ALA* 1.3 70.1 + - - +
83D PHE 3.3 1.6 - - - -
84D LYS* 3.1 6.3 + - - +
85D MET* 3.0 31.1 + - + +
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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