Contacts of the helix formed by residues 85 - 94 (chain A) in PDB entry 3MK4
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A MET 3.1 16.7 + - - +
82A GLN* 4.0 12.9 + - - +
83A GLN 3.7 1.0 - - - -
84A LEU* 1.3 70.3 - - - +
86A SER* 1.3 59.9 + - - +
87A GLU* 3.2 14.3 + - - +
88A SER* 2.8 47.4 + - - +
89A LEU* 4.0 11.8 + - - +
110A ILE* 4.0 4.0 - - - +
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Residues in contact with SER 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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84A LEU 3.2 2.4 + - - -
85A ASN* 1.3 71.4 - - - +
87A GLU* 1.3 67.4 + - - +
88A SER 3.1 0.9 - - - -
89A LEU* 3.0 8.3 + - - +
90A THR* 2.9 29.7 + - - -
107A LEU* 3.9 17.4 - - - +
110A ILE* 3.5 20.4 - - - +
111A SER 4.4 1.9 + - - -
114A ARG* 3.7 6.9 + - - -
330A ASN* 2.5 39.0 + - - -
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Residues in contact with GLU 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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81A MET* 4.5 16.8 - - + +
85A ASN* 3.2 9.5 + - - +
86A SER* 1.3 80.6 + - - +
88A SER* 1.3 57.7 + - - +
90A THR* 3.8 9.8 - - - +
91A ALA* 3.2 24.1 + - - +
114A ARG* 2.7 48.0 + - - -
330A ASN* 3.5 11.5 + - - +
334A HIS* 4.8 6.8 + - - +
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Residues in contact with SER 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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85A ASN* 2.8 41.1 + - - -
87A GLU* 1.3 76.6 - - - +
89A LEU* 1.3 64.8 - - - +
91A ALA* 3.2 16.7 + - - +
92A LEU* 3.2 19.6 + - - +
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Residues in contact with LEU 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 ASN 4.1 11.7 - - - +
86A SER* 3.0 7.8 + - - +
88A SER* 1.3 74.3 - - - +
90A THR* 1.3 66.9 + - - +
92A LEU* 3.2 22.4 + - + +
93A LEU* 3.1 25.2 + - - +
103A ILE* 3.7 21.5 - - + +
106A ASP* 3.8 40.8 - - + +
107A LEU* 3.8 29.2 - - + +
110A ILE* 4.2 12.8 - - + -
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Residues in contact with THR 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 SER 2.9 18.4 + - - -
87A GLU* 3.8 10.0 - - - +
89A LEU* 1.3 76.9 - - - +
91A ALA* 1.3 58.0 + - - +
93A LEU* 3.2 13.0 + - - +
94A LYS* 2.9 56.5 + - + +
107A LEU* 4.2 4.9 - - - +
330A ASN* 5.6 0.2 + - - -
26B LEU* 4.5 7.6 - - + -
29B PHE* 4.0 37.0 - - + -
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Residues in contact with ALA 91 (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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87A GLU 3.2 12.5 + - - +
88A SER* 3.2 13.7 + - - +
90A THR* 1.3 80.3 - - - +
92A LEU* 1.3 62.2 + - + +
94A LYS* 3.4 10.6 + - - +
95A ASN* 3.4 24.4 + - - +
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Residues in contact with LEU 92 (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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88A SER* 3.2 13.9 + - - +
89A LEU* 3.2 23.7 + - + +
91A ALA* 1.3 76.0 - - + +
93A LEU* 1.3 59.8 + - - +
95A ASN* 2.9 26.1 + - + +
97A PRO* 3.3 20.5 - - + +
103A ILE* 3.8 24.7 - - + -
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Residues in contact with LEU 93 (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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89A LEU 3.1 9.4 + - - +
90A THR* 3.2 7.4 + - - +
92A LEU* 1.3 71.5 - - - +
94A LYS* 1.3 59.1 + - - +
95A ASN 3.0 9.7 + - - -
96A ARG* 3.7 7.8 + - - -
97A PRO* 3.7 10.2 - - + +
100A LYS* 3.9 15.7 - - + +
103A ILE* 3.4 33.2 - - + -
104A TRP* 3.5 40.6 - - + +
107A LEU* 3.4 33.2 - - + -
26B LEU* 3.8 27.3 - - + +
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Residues in contact with LYS 94 (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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90A THR* 2.9 36.3 + - + +
91A ALA* 3.6 8.1 - - - +
92A LEU 3.3 0.2 - - - -
93A LEU* 1.3 74.0 - - - +
95A ASN* 1.3 70.5 + - - +
96A ARG 3.8 1.6 - - - -
26B LEU* 3.7 42.3 + - + -
27B ASP* 5.8 0.7 - - - +
29B PHE* 5.0 9.1 - - - +
30B ASP* 5.6 2.6 - - - +
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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