Contacts of the helix formed by residues 91 - 101 (chain A) in PDB entry 5BOL
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 ASP 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LYS* 3.1 9.5 + - + +
88A ILE* 3.1 15.1 + - - +
90A GLN* 1.3 75.7 - - - +
92A ASP* 1.3 68.4 + - - +
93A THR* 3.2 11.0 + - - -
94A SER* 2.8 37.6 + - - +
95A SER* 2.9 24.8 + - - -
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Residues in contact with ASP 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 GLN 3.5 8.4 + - - +
91A ASP* 1.3 71.7 + - - +
93A THR* 1.3 58.2 + - - +
95A SER* 3.4 5.8 + - - -
96A SER* 2.9 36.9 + - - +
120A LYS* 5.6 6.1 - - - +
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Residues in contact with THR 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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29A VAL* 6.0 0.7 - - + -
91A ASP* 3.3 9.9 + - - +
92A ASP* 1.3 78.5 - - - +
94A SER* 1.3 60.8 + - - +
96A SER* 3.3 5.4 + - - -
97A ILE* 2.9 49.1 + - + +
112A ARG* 4.7 11.7 - - - +
115A VAL* 4.8 15.1 - - + +
120A LYS* 5.4 3.4 + - - +
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Residues in contact with SER 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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25A PHE* 3.9 6.6 - - - -
29A VAL* 3.6 34.4 - - - +
88A ILE* 4.0 23.6 - - - +
91A ASP* 2.8 30.0 + - - +
93A THR* 1.3 73.5 - - - +
95A SER* 1.3 58.3 + - - +
97A ILE* 3.9 2.0 - - - +
98A ASN* 2.9 36.8 + - - +
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Residues in contact with SER 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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88A ILE 4.0 2.1 + - - -
89A ARG* 3.2 25.3 + - - -
91A ASP 2.9 20.3 + - - -
92A ASP* 3.6 6.3 - - - -
94A SER* 1.3 76.5 - - - +
96A SER* 1.3 63.8 - - - +
98A ASN* 3.7 7.4 - - - +
99A PHE* 3.0 23.4 + - - +
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Residues in contact with SER 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 ASP* 2.9 21.4 + - - +
93A THR* 3.6 6.1 - - - -
95A SER* 1.3 76.6 - - - +
97A ILE* 1.3 63.3 + - - +
99A PHE* 3.1 7.6 + - - +
100A LEU* 3.0 26.0 + - - +
115A VAL* 3.8 22.7 - - - -
120A LYS* 3.8 34.8 + - - +
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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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28A ASN* 3.4 29.2 - - + +
29A VAL* 4.5 6.1 - - + -
93A THR* 2.9 32.2 + - + +
94A SER 4.0 2.9 - - - +
96A SER* 1.3 75.7 - - - +
98A ASN* 1.3 63.6 + - - +
100A LEU* 3.4 0.9 + - - -
101A THR* 3.1 25.3 + - + +
108A PRO 4.5 2.0 - - - +
111A ALA* 3.7 20.1 - - + +
112A ARG* 3.5 54.1 - - + +
115A VAL* 3.9 19.5 - - + -
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Residues in contact with ASN 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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24A ASN* 3.9 8.8 - - - +
25A PHE* 4.7 8.3 - - - +
28A ASN* 2.9 32.6 + - - +
29A VAL* 4.0 12.3 - - - +
88A ILE* 4.8 12.1 - - - +
94A SER 2.9 23.3 + - - +
95A SER* 3.7 6.8 - - - +
97A ILE* 1.3 76.2 - - - +
99A PHE* 1.3 62.1 + - - +
101A THR* 2.7 20.1 + - - -
102A ARG* 3.5 12.8 - - - +
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Residues in contact with PHE 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 SER 3.0 13.8 + - - +
96A SER* 3.5 7.0 - - - +
98A ASN* 1.3 75.5 - - - +
100A LEU* 1.3 72.5 + - + +
102A ARG* 2.8 55.1 + - - +
103A VAL* 4.1 3.1 + - + +
120A LYS 4.0 15.0 - - - -
121A THR* 3.9 6.3 - - - -
122A LEU* 3.5 45.5 - - + -
125A LEU* 5.0 4.0 - - + -
143A PHE* 3.7 30.5 - + - -
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Residues in contact with LEU 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 SER 3.0 16.4 + - - +
97A ILE 3.4 3.6 + - - +
99A PHE* 1.3 89.5 - - + +
101A THR* 1.3 59.0 + - - +
102A ARG 3.0 5.4 + - - -
103A VAL* 3.0 22.9 + - - +
106A ILE* 3.5 13.6 - - + +
111A ALA* 3.6 21.5 - - + +
114A PHE* 3.8 8.7 - - + -
115A VAL* 3.5 24.7 - - + -
119A ILE 3.4 22.0 - - - +
120A LYS* 4.1 14.8 - - - -
125A LEU* 3.7 35.7 - - + -
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Residues in contact with THR 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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28A ASN* 3.3 39.5 + - + +
97A ILE* 3.1 14.1 + - + +
98A ASN 2.7 20.8 + - - -
100A LEU* 1.3 75.1 - - - +
102A ARG* 1.3 57.2 + - - +
103A VAL 3.1 0.9 - - - -
106A ILE 3.3 11.4 - - - -
107A GLY* 3.8 16.2 - - - +
108A PRO* 4.0 3.1 - - + -
111A ALA* 3.6 18.2 - - + -
402P NA 2.3 26.0 - - - -
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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