Contacts of the helix formed by residues 90 - 101 (chain A) in PDB entry 1O0W
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 SER 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A SER 3.4 12.0 + - - -
87A ALA* 2.9 23.1 + - - -
88A ALA 3.3 1.2 - - - -
89A ALA* 1.3 82.1 - - - +
91A GLU* 1.3 65.9 + - - +
92A GLU* 3.8 10.4 + - - +
93A VAL* 3.2 16.1 + - - +
94A LEU* 3.0 22.0 + - - +
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Residues in contact with GLU 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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89A ALA 3.9 0.6 + - - -
90A SER* 1.3 72.7 - - - +
92A GLU* 1.3 57.5 + - - +
94A LEU* 3.3 2.1 + - - +
95A ALA* 2.8 34.7 + - - +
122A ASP* 3.7 23.5 - - + +
123A SER* 3.5 28.8 + - - -
126A ALA* 3.8 24.8 - - + +
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Residues in contact with GLU 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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90A SER* 3.8 10.3 + - - +
91A GLU* 1.3 79.4 - - - +
93A VAL* 1.3 64.2 + - + +
95A ALA* 3.9 4.9 - - - +
96A MET* 3.1 22.5 + - - +
122A ASP* 5.0 7.6 - - - +
166A LEU 4.3 13.2 - - - +
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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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87A ALA 3.2 24.2 - - - +
88A ALA* 3.4 25.1 - - - +
90A SER* 3.2 7.8 + - - +
92A GLU* 1.3 79.7 - - + +
94A LEU* 1.3 59.7 + - + +
96A MET* 3.0 14.6 + - + +
97A VAL* 2.8 32.6 + - + +
153A PHE* 4.3 5.2 - - + -
156A TYR* 4.2 25.1 - - + -
160A ILE* 4.6 1.3 - - + -
166A LEU* 3.9 24.0 - - + -
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Residues in contact with LEU 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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61A LEU* 3.5 34.5 - - + -
88A ALA 4.3 6.1 - - - +
89A ALA 3.8 8.5 - - - +
90A SER 3.0 18.9 + - - +
91A GLU* 3.8 3.6 - - - +
93A VAL* 1.3 76.8 - - - +
95A ALA* 1.3 57.4 + - - +
97A VAL* 3.3 5.1 + - - +
98A SER* 2.8 32.8 + - - -
126A ALA* 3.9 20.4 - - + +
129A PHE* 4.0 20.7 - - + +
130A GLU* 3.6 26.7 - - + +
153A PHE* 4.1 24.5 - - + -
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Residues in contact with ALA 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 GLU 2.8 20.8 + - - +
92A GLU 3.9 3.6 - - - +
94A LEU* 1.3 69.6 - - - +
96A MET* 1.3 61.5 + - - +
98A SER* 3.2 8.1 + - - -
99A ARG* 2.8 57.1 + - - +
122A ASP* 3.9 31.0 - - - +
125A LEU* 4.5 6.1 - - + -
126A ALA* 4.4 2.2 - - - +
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Residues in contact with MET 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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92A GLU 3.1 14.5 + - - +
93A VAL* 3.0 20.6 + - + +
95A ALA* 1.3 77.0 - - - +
97A VAL* 1.3 63.4 + - + +
99A ARG* 3.2 9.2 + - - +
100A LYS* 3.0 37.4 + - + +
156A TYR* 3.6 48.0 - - + +
166A LEU* 4.1 16.8 - - + +
167A PHE* 3.8 36.6 - - - +
168A ASP* 4.0 12.3 - - + +
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Residues in contact with VAL 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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93A VAL* 2.8 19.9 + - + +
94A LEU* 3.6 9.4 - - - +
96A MET* 1.3 76.1 - - + +
98A SER* 1.3 63.2 + - - +
100A LYS* 3.3 16.7 + - - +
101A MET* 3.3 18.3 + - + +
129A PHE* 3.6 33.9 - - + -
149A PHE* 5.2 0.2 - - + -
152A GLU* 3.9 20.2 - - - +
153A PHE* 3.9 15.0 - - + -
156A TYR* 3.5 33.9 - - + +
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Residues in contact with SER 98 (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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94A LEU 2.8 26.0 + - - -
95A ALA 3.2 5.1 + - - -
97A VAL* 1.3 75.3 - - - +
99A ARG* 1.3 61.8 + - - +
101A MET* 3.1 9.4 + - - +
103A LEU* 3.0 44.6 + - - +
125A LEU* 3.2 36.8 + - - -
129A PHE* 3.4 15.3 - - - +
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Residues in contact with ARG 99 (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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95A ALA* 2.8 39.1 + - - +
96A MET* 3.7 7.9 - - - +
98A SER* 1.3 71.6 - - - +
100A LYS* 1.3 59.7 + - + +
102A ASN* 2.8 22.6 + - - +
103A LEU 4.8 0.4 - - - +
120A ASP* 2.8 27.9 + - - +
122A ASP* 2.7 31.9 + - - -
125A LEU* 3.5 24.4 - - + +
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Residues in contact with LYS 100 (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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96A MET* 3.0 26.9 + - + +
97A VAL* 3.5 11.2 - - - +
99A ARG* 1.3 77.7 - - + +
101A MET* 1.3 58.0 - - - +
102A ASN* 3.3 1.3 + - - +
152A GLU* 5.2 5.8 - - - +
156A TYR* 5.2 7.2 - - - +
168A ASP* 3.1 42.4 + - - +
170A LYS* 5.2 9.9 - - - +
171A THR* 4.8 1.2 + - - -
221A LYS* 6.0 0.5 + - - -
225A LYS* 5.1 17.2 - - - +
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Residues in contact with MET 101 (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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12A PHE* 5.1 0.7 - - + -
16A THR* 4.0 26.3 - - + +
18A ILE* 5.0 6.1 - - + -
97A VAL* 3.6 11.9 - - + +
98A SER 3.1 9.4 + - - +
99A ARG 3.0 0.6 - - - -
100A LYS* 1.3 77.8 - - - +
102A ASN* 1.3 70.6 + - - +
103A LEU* 4.2 17.7 - - + +
106A PHE* 4.1 8.8 - - - -
129A PHE* 3.4 30.5 - - + -
132A LEU* 4.0 22.9 - - - -
149A PHE* 4.1 16.6 - - + -
152A GLU* 5.9 0.4 - - - +
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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