Contacts of the helix formed by residues 80 - 90 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS* 4.9 4.8 - - - +
77A LYS* 3.1 18.9 + - - +
78A SER 4.0 10.5 + - - -
79A ARG* 1.3 81.0 - - - +
81A VAL* 1.3 65.4 + - - +
82A GLU 3.3 2.9 + - - +
83A LYS* 3.4 28.6 + - + +
84A ALA* 3.0 22.5 + - - +
506A VAL* 4.4 0.2 - - - -
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ALA* 3.2 35.5 + - + +
79A ARG 4.6 1.6 - - - +
80A ASN* 1.3 73.8 - - - +
82A GLU* 1.3 60.3 + - + +
84A ALA* 3.3 2.9 + - - +
85A ARG* 2.8 28.9 + - + +
310A PHE* 5.1 6.5 - - + -
315A LEU* 4.7 7.0 - - + -
321A VAL* 4.3 14.1 - - + -
502A PHE* 4.4 3.5 - - + -
503A THR* 4.0 38.1 - - + +
506A VAL* 4.2 20.6 - - + -
507A ILE* 4.2 11.0 - - + -
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS* 5.2 5.5 - - - +
80A ASN 3.3 1.0 - - - -
81A VAL* 1.3 77.9 - - + +
83A LYS* 1.3 57.4 + - - +
85A ARG* 3.3 36.5 + - - +
86A ASP* 3.0 35.7 + - - +
313A ALA 5.0 1.0 - - - +
314A PRO* 5.0 4.5 - - - +
315A LEU* 3.9 43.9 + - + +
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASN* 3.4 33.0 + - + +
81A VAL 3.4 0.2 - - - -
82A GLU* 1.3 76.9 - - - +
84A ALA* 1.3 62.0 - - - +
86A ASP* 3.3 9.2 + - - +
87A ALA* 3.0 24.6 + - + +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LYS* 5.8 1.1 - - - +
80A ASN 3.0 18.3 + - - +
81A VAL 3.6 3.6 - - - +
83A LYS* 1.3 77.2 - - - +
85A ARG* 1.3 63.3 + - - +
87A ALA* 3.2 9.0 + - - +
88A MET 3.0 17.7 + - - -
94A ILE* 4.9 2.3 - - - +
502A PHE* 3.5 10.0 - - + -
506A VAL* 3.7 33.4 - - + -
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 2.8 15.3 + - + +
82A GLU* 3.5 42.5 + - - +
84A ALA* 1.3 76.5 - - - +
86A ASP* 1.3 89.4 + - - +
88A MET* 3.1 3.0 + - - +
89A PHE* 3.1 34.6 + - + -
310A PHE* 2.9 64.6 + - + -
311A CYS* 3.4 32.5 + - - +
313A ALA 4.6 4.4 + - - -
315A LEU* 5.8 0.6 - - - +
318A ASN* 4.3 6.5 - - - +
502A PHE* 3.6 17.6 - - + -
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 3.0 21.2 + - - +
83A LYS* 3.3 7.5 + - - +
84A ALA 3.3 0.2 - - - -
85A ARG* 1.3 109.6 + - - +
87A ALA* 1.3 56.9 + - - +
89A PHE* 3.3 6.4 + - - +
90A ALA* 2.9 32.0 + - - +
311A CYS* 4.8 7.8 - - - -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS* 3.0 14.0 + - + +
84A ALA* 3.4 12.1 - - - +
85A ARG 3.1 0.2 - - - -
86A ASP* 1.3 77.2 - - - +
88A MET* 1.3 62.9 + - - +
90A ALA* 3.4 1.1 + - - -
91A GLY 3.3 2.6 + - - -
92A GLU* 3.0 59.6 + - - +
94A ILE* 4.0 13.9 - - + -
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA 3.0 10.3 + - - +
85A ARG 3.5 6.1 - - - +
87A ALA* 1.3 77.8 - - - +
89A PHE* 1.3 87.9 + - + +
91A GLY* 3.0 13.0 + - - -
92A GLU 5.1 1.1 - - - +
94A ILE* 3.7 22.3 - - + +
102A VAL* 3.3 37.7 + - - +
103A LEU* 3.4 12.8 - - - +
104A HIS* 4.3 12.1 - - - +
105A VAL* 4.5 8.3 - - + -
310A PHE* 4.6 1.3 - - + -
499A HIS* 4.0 22.7 - - + +
502A PHE* 3.9 34.1 - - + -
513A PHE* 4.4 1.1 - - - -
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 3.1 42.3 + - + +
86A ASP* 3.9 6.3 - - - +
88A MET* 1.3 104.6 - - + +
90A ALA* 1.3 59.4 + - - +
91A GLY 3.5 0.7 + - - -
103A LEU* 4.3 0.9 - - - +
105A VAL* 3.8 29.2 - - + -
113A ARG* 3.0 49.5 + - - +
115A ILE* 4.1 8.7 - - - +
307A ASP* 3.8 39.7 - - + -
308A ASN* 5.8 1.3 - - - -
310A PHE* 3.9 7.6 - + - -
311A CYS* 4.9 14.6 - - + -
499A HIS* 4.2 4.7 - - - -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP 2.9 17.2 + - - +
87A ALA* 3.4 6.3 + - - +
88A MET 3.1 0.2 - - - -
89A PHE* 1.3 78.4 - - - +
91A GLY* 1.3 60.4 + - - +
92A GLU* 3.3 12.0 + - + +
113A ARG* 5.0 2.7 - - - +
115A ILE* 4.6 5.9 - - - +
116A MET* 4.4 10.2 + - - +
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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