Contacts of the helix formed by residues 87 - 95 (chain A) in PDB entry 6M0X
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A LEU* 1.3 73.1 - - - +
88A PRO* 1.3 67.3 - - - +
89A TYR* 3.0 25.1 + - - +
90A GLN* 3.3 29.9 + - + +
91A LEU* 3.3 17.8 + - - +
156A LEU* 3.8 13.1 - - - +
159A TYR* 3.2 35.0 - - + -
45B A 5.6 1.3 - - - -
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Residues in contact with PRO 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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86A LEU 3.1 12.3 - - - +
87A ASN* 1.3 87.3 - - - +
89A TYR* 1.3 63.4 + - + +
91A LEU* 3.3 5.2 + - + +
92A ARG* 2.9 34.9 + - - +
107A ILE* 3.7 27.6 - - + +
108A ALA* 4.3 1.5 - - - +
111A ASN* 3.6 33.2 - - + -
45B A 4.6 3.1 - - - +
46B A 3.8 34.8 - - - +
47B A 5.9 0.2 - - - +
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Residues in contact with TYR 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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87A ASN* 3.0 14.9 + - - +
88A PRO* 1.3 84.3 - - + +
90A GLN* 1.3 60.7 + - - +
92A ARG* 3.4 16.4 - - - +
93A VAL* 3.2 26.3 + - - +
111A ASN* 3.5 23.5 + - - -
115A HIS* 4.5 7.4 - + - -
152A GLY 4.3 2.6 - - - +
155A GLN* 3.2 47.5 + - + -
156A LEU* 4.0 20.1 - - + +
159A TYR* 4.7 4.0 - + + -
165A LEU* 3.4 29.5 - - + +
166A ARG* 4.1 6.8 - - - -
182A ASN* 4.7 3.6 + - - -
45B A 3.9 4.5 - - - -
46B A 2.7 29.5 + - - -
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Residues in contact with GLN 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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87A ASN* 3.3 28.8 + - - +
88A PRO 3.2 0.8 - - - -
89A TYR* 1.3 77.7 - - - +
91A LEU* 1.3 79.2 + - - +
93A VAL* 3.0 3.5 + - + +
94A LYS* 2.8 41.4 + - + +
156A LEU* 3.5 24.2 - - + +
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Residues in contact with LEU 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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86A LEU* 4.4 19.1 - - + -
87A ASN 3.3 20.4 - - - +
88A PRO* 3.3 9.9 + - + +
90A GLN* 1.3 91.4 - - - +
92A ARG* 1.3 58.8 + - - +
93A VAL 3.1 0.2 - - - -
94A LYS* 3.8 11.4 - - + -
95A GLY* 2.9 23.4 + - - -
100A LEU* 3.4 21.5 - - + +
104A GLU* 3.9 60.8 - - + +
107A ILE* 4.4 6.1 - - + -
108A ALA* 4.3 3.6 - - + -
196A ILE* 5.3 0.2 - - - +
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Residues in contact with ARG 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 PRO 2.9 20.3 + - - +
89A TYR* 3.4 15.0 - - - +
91A LEU* 1.3 78.9 - - - +
93A VAL* 1.3 58.8 + - - +
95A GLY 4.4 0.4 - - - -
96A LEU* 4.1 9.2 + - - +
108A ALA* 3.5 22.4 - - + +
111A ASN* 2.2 35.0 + - - -
112A MET* 3.4 37.4 - - - +
150A THR* 5.0 0.5 + - - -
152A GLY* 3.2 18.7 - - - +
155A GLN* 2.4 31.3 + - - -
189A TYR* 4.2 7.7 - - - -
192A GLU* 2.5 30.2 + - - +
196A ILE* 3.5 27.2 - - - +
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Residues in contact with VAL 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 TYR 3.2 16.8 - - - +
90A GLN* 3.0 6.8 + - + +
92A ARG* 1.3 79.9 - - - +
94A LYS* 1.3 66.0 + - - +
95A GLY 3.3 0.2 - - - -
96A LEU* 3.1 22.8 - - + +
97A THR* 4.0 4.9 + - - +
152A GLY 4.1 0.4 - - - -
153A GLN* 3.7 49.6 - - + +
156A LEU* 3.9 20.2 - - + -
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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 GLN* 2.8 32.8 + - + +
91A LEU* 4.2 12.8 - - + +
93A VAL* 1.3 73.8 - - - +
95A GLY* 1.3 54.0 + - - +
97A THR* 3.0 6.1 + - - -
98A ASP* 2.6 53.5 + - + +
99A GLU 3.5 17.9 - - - -
100A LEU* 3.6 19.7 - - + -
104A GLU* 5.0 6.3 - - - +
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Residues in contact with GLY 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 LEU 2.9 18.8 + - - -
94A LYS* 1.3 77.0 - - - +
96A LEU* 1.3 60.5 + - - +
97A THR 3.2 0.9 + - - -
98A ASP 3.3 11.0 - - - +
100A LEU* 3.5 19.0 - - - +
196A ILE* 3.7 12.7 - - - +
199A THR* 3.6 14.4 - - - +
200A GLN* 3.4 14.8 - - - +
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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