Contacts of the helix formed by residues 85 - 97 (chain A) in PDB entry 1M6X
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 LYS 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A THR* 3.8 43.2 + - + +
83A THR* 3.6 13.2 + - - +
84A GLN* 1.3 78.8 - - - +
86A ALA* 1.3 65.4 + - - +
87A THR* 3.3 3.4 - - - -
88A ILE* 3.3 44.1 + - + +
89A LEU* 3.5 9.0 + - - +
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Residues in contact with ALA 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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83A THR* 4.2 9.4 + - + -
84A GLN* 3.3 4.5 + - - +
85A LYS* 1.3 74.7 - - - +
87A THR* 1.3 65.4 + - - +
89A LEU* 2.9 8.6 + - - +
90A GLU* 2.8 31.4 + - - +
104A ILE* 3.5 35.4 - - + +
106A PRO* 5.0 11.2 - - + -
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Residues in contact with THR 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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85A LYS* 3.3 1.7 - - - -
86A ALA* 1.3 77.4 - - - +
88A ILE* 1.3 68.1 + - + +
90A GLU* 2.9 15.8 + - + +
91A ALA* 2.9 26.2 + - + +
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Residues in contact with ILE 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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45A ILE* 5.3 7.0 - - + -
46A THR* 6.4 1.6 - - + -
85A LYS* 3.3 44.1 + - + +
87A THR* 1.3 79.6 - - + +
89A LEU* 1.3 61.1 + - - +
91A ALA* 3.6 7.1 + - - +
92A SER* 3.0 31.3 + - - +
114C SER 6.0 4.0 - - - +
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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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42A CYS* 3.7 40.6 - - + +
45A ILE* 3.6 42.6 - - + -
46A THR* 4.0 13.0 - - + -
81A TYR* 4.2 13.2 - - + -
83A THR* 4.4 6.1 - - + -
85A LYS 3.5 6.6 + - - +
86A ALA 2.9 10.2 + - - +
88A ILE* 1.3 79.4 - - - +
90A GLU* 1.3 65.6 + - - +
92A SER* 3.2 6.6 + - - -
93A LEU* 2.9 28.3 + - + +
104A ILE* 3.9 26.9 - - + -
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Residues in contact with GLU 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 ALA* 2.8 32.0 + - - +
87A THR* 2.9 12.6 + - + +
89A LEU* 1.3 75.5 - - - +
91A ALA* 1.3 64.3 + - - +
93A LEU* 3.3 4.9 + - - +
94A LYS* 3.0 23.3 + - - +
101A GLU* 4.9 2.1 - - - +
102A PHE* 2.7 39.9 + - + +
103A THR* 3.6 8.0 + - - +
104A ILE* 3.3 35.0 + - + +
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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 THR* 2.9 14.8 + - + +
88A ILE* 3.6 11.9 - - - +
90A GLU* 1.3 77.3 - - - +
92A SER* 1.3 63.4 + - - +
94A LYS* 3.0 9.7 + - - +
95A LYS* 3.0 30.7 + - - +
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Residues in contact with SER 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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45A ILE* 3.4 32.7 - - - +
88A ILE* 3.0 16.6 + - - +
89A LEU 3.2 8.9 + - - -
91A ALA* 1.3 78.1 - - - +
93A LEU* 1.3 64.2 + - - +
95A LYS* 3.1 21.6 + - - +
96A LEU 3.4 3.1 + - - -
114C SER 4.9 8.5 + - - -
116C ILE* 2.9 27.4 + - - +
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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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19A PHE* 4.7 8.1 - - + -
38A LEU* 4.0 17.3 - - + -
41A LEU* 4.5 20.0 - - + -
42A CYS* 4.4 6.7 - - - -
45A ILE* 4.5 15.5 - - + -
79A PHE* 3.9 11.9 - - + -
89A LEU* 2.9 17.6 + - + +
90A GLU 3.6 7.0 - - - +
92A SER* 1.3 75.3 - - - +
94A LYS* 1.3 62.1 + - - +
96A LEU* 3.0 20.5 + - + +
97A ILE* 3.2 5.4 + - - +
102A PHE* 3.8 36.8 - - + -
104A ILE* 3.8 29.6 - - + -
116C ILE* 3.8 4.7 - - + +
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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 GLU 3.0 12.9 + - - +
91A ALA* 3.0 12.1 + - - +
93A LEU* 1.3 72.0 - - - +
95A LYS* 1.3 56.8 + - - +
96A LEU 2.9 2.0 - - - -
97A ILE 2.6 26.5 + - - -
98A PRO* 2.7 48.1 + - + +
100A TRP 3.2 16.6 + - - +
101A GLU* 3.4 25.8 + - - +
102A PHE* 3.8 9.1 - - + +
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Residues in contact with LYS 95 (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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91A ALA* 3.0 23.3 + - - +
92A SER* 3.1 13.2 + - - +
94A LYS* 1.3 76.3 - - - +
96A LEU* 1.3 60.6 + - - +
98A PRO* 3.7 15.0 - - - +
114C SER 4.9 6.5 + - - -
115C ASP* 3.6 30.8 + - - +
116C ILE* 5.3 4.9 - - + +
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Residues in contact with LEU 96 (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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16A VAL* 3.8 34.1 - - + -
19A PHE* 4.0 10.8 - - + -
20A VAL* 4.4 18.6 - - + +
41A LEU* 3.9 26.2 - - + -
92A SER 3.4 4.2 + - - +
93A LEU* 3.0 16.1 + - + +
94A LYS 2.9 0.4 - - - -
95A LYS* 1.3 82.0 - - - +
97A ILE* 1.3 65.2 + - + +
98A PRO* 3.7 3.3 - - - +
116C ILE* 4.4 24.7 - - + +
117C THR* 4.4 22.2 - - + -
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Residues in contact with ILE 97 (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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19A PHE* 3.6 28.7 - - + +
20A VAL* 4.4 12.1 - - + -
23A PHE* 3.4 43.5 - - + -
93A LEU 3.2 2.6 + - - +
94A LYS* 2.6 16.2 + - - +
96A LEU* 1.3 86.4 - - + +
98A PRO* 1.3 60.5 - - + +
99A ALA* 3.2 4.7 - - + +
100A TRP* 3.0 52.4 + - + +
102A PHE* 3.9 10.3 - - + -
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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