Contacts of the helix formed by residues 80 - 90 (chain B) in PDB entry 4WMJ
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 ASN 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 4.2 5.4 - - - +
76B ALA 3.3 0.6 + - - -
77B LYS 2.9 18.5 + - - +
78B SER 3.1 10.7 + - - -
79B ARG* 1.3 82.3 - - - +
81B VAL* 1.3 65.3 + - - +
82B GLU 3.4 2.9 + - - +
83B LYS* 3.6 27.9 + - + +
84B ALA* 3.1 21.8 + - - +
506B VAL* 4.3 0.2 - - - -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 3.1 32.3 + - + +
79B ARG 4.6 1.3 - - - +
80B ASN* 1.3 74.7 - - - +
82B GLU* 1.3 60.2 + - + +
84B ALA* 3.3 1.6 + - - +
85B ARG* 2.8 29.9 + - + +
310B PHE* 5.0 6.5 - - + -
315B LEU* 4.6 8.5 - - + -
321B VAL* 4.3 14.8 - - + -
502B PHE* 4.5 2.4 - - + -
503B THR* 3.9 40.4 - - + +
506B VAL* 4.1 17.3 - - + -
507B ILE* 4.1 15.5 - - + -
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 5.0 7.3 - - - +
80B ASN 3.4 0.6 - - - -
81B VAL* 1.3 74.6 - - + +
83B LYS* 1.3 64.1 + - - +
85B ARG* 3.3 35.2 + - - +
86B ASP* 2.9 30.7 + - - +
313B ALA 4.9 3.5 - - - +
314B PRO* 5.0 2.8 - - - +
315B LEU* 3.7 49.3 + - + +
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Residues in contact with LYS 83 (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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2B GLU* 3.3 27.2 + - - -
80B ASN* 3.6 31.1 + - + +
82B GLU* 1.3 78.9 - - - +
84B ALA* 1.3 56.5 + - - +
86B ASP* 3.3 8.5 + - - +
87B ALA* 3.0 27.8 + - + +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LYS* 5.2 2.5 - - - +
80B ASN 3.1 18.0 + - - +
81B VAL 3.6 4.5 - - - +
83B LYS* 1.3 72.2 - - - +
85B ARG* 1.3 67.0 + - - +
87B ALA* 3.2 8.9 + - - +
88B MET* 3.1 17.0 + - - +
94B ILE* 5.0 2.4 - - - +
502B PHE* 3.6 9.4 - - + -
506B VAL* 3.7 33.0 - - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 2.8 14.0 + - + +
82B GLU* 3.4 44.8 + - - +
84B ALA* 1.3 73.0 - - - +
86B ASP* 1.3 90.1 + - - +
88B MET* 3.0 4.4 + - - +
89B PHE* 3.0 38.2 + - + -
310B PHE* 2.9 58.2 + - + -
311B CYS* 3.5 30.2 + - - +
313B ALA 4.6 3.2 + - - -
315B LEU* 5.6 0.8 - - - +
318B ASN* 4.4 6.3 - - - +
502B PHE* 3.6 18.0 - - + -
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Residues in contact with ASP 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 GLU* 2.9 20.8 + - - +
83B LYS* 3.7 7.3 - - - +
85B ARG* 1.3 110.9 + - - +
87B ALA* 1.3 58.9 + - - +
89B PHE* 3.4 5.9 + - - +
90B ALA* 2.9 32.6 + - - +
311B CYS* 5.3 3.6 - - - +
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Residues in contact with ALA 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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83B LYS* 3.0 13.6 + - + +
84B ALA* 3.4 12.3 - - - +
85B ARG 3.1 0.2 - - - -
86B ASP* 1.3 74.7 - - - +
88B MET* 1.3 65.6 + - - +
90B ALA 3.3 4.7 + - - -
92B GLU* 3.0 58.4 + - - +
94B ILE* 4.0 14.6 - - + -
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA 3.1 9.8 + - - +
85B ARG 3.0 6.5 + - - +
87B ALA* 1.3 74.9 - - - +
89B PHE* 1.3 84.0 + - + +
91B GLY* 3.0 18.5 + - - -
92B GLU 4.4 1.6 + - - +
94B ILE* 3.8 23.1 - - + +
102B VAL* 3.2 38.8 - - - +
103B LEU* 3.4 11.8 - - - +
104B HIS* 4.3 12.1 - - - -
105B VAL* 4.7 7.0 - - + -
310B PHE* 4.5 0.9 - - + -
499B HIS* 4.0 23.8 - - + +
502B PHE* 3.9 35.0 - - + -
513B PHE* 4.3 1.8 - - - -
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Residues in contact with PHE 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 ARG* 3.0 31.3 + - + +
86B ASP* 3.9 5.8 - - - +
88B MET* 1.3 102.4 - - + +
90B ALA* 1.3 60.1 + - - +
91B GLY 3.5 0.5 + - - -
103B LEU* 4.2 1.5 - - - +
105B VAL* 3.5 33.7 - - + -
113B ARG* 3.0 51.9 + - - +
115B ILE* 4.1 8.8 - - - +
307B ASP* 3.8 27.1 - - + -
308B ASN* 5.9 0.9 - - - -
310B PHE* 4.1 5.8 - + - -
311B CYS* 3.5 31.4 - - - -
499B HIS* 4.2 5.2 - + - -
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Residues in contact with ALA 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 ASP 2.9 18.8 + - - +
87B ALA* 3.8 7.2 - - - +
88B MET 3.2 0.4 - - - -
89B PHE* 1.3 76.0 - - - +
91B GLY* 1.3 59.8 + - - +
92B GLU* 3.4 12.8 + - + +
113B ARG* 5.0 2.9 - - - +
115B ILE* 4.6 3.8 - - - -
116B MET* 4.2 15.8 + - - +
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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