Contacts of the helix formed by residues 83 - 90 (chain B) in PDB entry 3D9M
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 VAL 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ILE* 3.9 13.9 - - + -
40B TYR* 3.6 50.8 - - + +
81B LYS 3.7 11.9 - - - +
82B ASP* 1.3 72.8 - - - +
84B PHE* 1.3 66.6 + - + +
86B PRO* 3.6 6.3 - - - +
87B ARG* 3.3 24.3 + - - +
401B NH4 3.0 22.1 + - - +
509B SO4 4.7 1.0 + - - -
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA 3.8 19.3 - - - -
34B ILE* 4.2 10.3 - - + -
37B ILE* 3.5 26.2 - - + -
40B TYR* 3.8 26.5 - - + -
43B VAL* 3.7 26.9 - - + -
44B VAL* 4.0 16.4 - - + -
69B ILE* 3.5 28.0 - - + -
70B VAL* 4.1 10.5 - - + -
73B SER* 3.6 22.9 - - - -
82B ASP* 2.8 9.5 + - - +
83B VAL* 1.3 80.9 - - + +
85B ALA* 1.3 59.7 + - - +
87B ARG* 3.1 2.7 + - - +
88B PHE* 2.8 39.7 + + + -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B VAL* 3.8 23.4 - - + +
74B ARG* 5.1 1.6 - - - +
82B ASP* 3.0 19.5 + - - +
84B PHE* 1.3 73.6 - - - +
86B PRO* 1.4 69.2 - - + +
88B PHE 3.3 0.2 + - - -
89B SER* 2.9 25.6 + - - -
122B VAL 3.9 16.6 - - - +
123B PHE* 3.4 20.7 - - + -
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Residues in contact with PRO 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ASP* 3.4 25.8 - - - +
83B VAL* 3.6 6.3 - - - +
84B PHE 3.5 2.2 - - - -
85B ALA* 1.4 94.1 - - + +
87B ARG* 1.3 58.2 + - - +
89B SER* 2.4 30.2 + - - +
90B ASN* 3.2 9.2 - - - +
509B SO4 4.0 12.0 + - - +
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 4.0 15.9 - - + -
41B LYS* 3.6 31.1 + - - +
44B VAL* 3.6 33.2 - - + +
48B GLU* 4.6 1.0 - - - +
83B VAL 3.3 16.6 + - - +
84B PHE 3.1 3.8 + - - +
86B PRO* 1.3 77.1 - - - +
88B PHE* 1.3 64.6 + - - +
90B ASN* 3.2 29.8 + - - +
91B ASN 4.5 0.7 + - - -
504B SO4 2.8 42.4 + - - -
509B SO4 2.8 47.7 + - - +
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL 5.3 0.4 - - - -
44B VAL* 3.7 37.9 - - + -
47B VAL* 3.8 28.9 - - + -
48B GLU* 4.1 12.8 - - + +
66B ILE* 3.7 43.1 - - + -
69B ILE* 4.4 10.5 - - + -
70B VAL* 3.7 23.1 - - + -
84B PHE* 2.8 42.5 + + + +
85B ALA 3.8 3.4 - - - +
87B ARG* 1.3 72.5 - - - +
89B SER* 1.3 61.6 + - - +
90B ASN 3.3 0.7 + - - -
91B ASN 3.8 2.3 + - - -
92B ILE* 3.5 23.0 + - + +
95B THR* 5.0 1.9 + - + -
123B PHE* 4.2 14.4 - - + -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA 2.9 13.1 + - - -
86B PRO* 2.4 28.6 + - - +
88B PHE* 1.3 78.0 - - - +
90B ASN* 1.3 67.7 + - - +
92B ILE* 3.3 29.2 + - - +
123B PHE* 4.3 9.6 - - - -
127B ILE* 4.7 21.1 - - - +
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Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PRO 3.2 11.8 - - - +
87B ARG* 3.5 30.2 - - - +
88B PHE 3.2 1.0 - - - -
89B SER* 1.3 82.0 + - - +
91B ASN* 1.3 70.7 + - - +
92B ILE 3.7 0.2 + - - -
93B ILE 5.3 0.3 + - - -
509B SO4 3.0 27.1 + - - -
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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