Contacts of the helix formed by residues 94 - 100 (chain A) in PDB entry 2BME
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ASP* 2.9 21.1 + - - +
92A ILE 3.3 0.6 - - - -
93A THR* 1.3 80.8 - - - +
95A ARG* 1.3 65.7 + - - +
96A GLU* 4.0 10.0 + - - +
97A THR* 2.8 42.7 + - - +
98A TYR* 3.5 2.8 + - - +
132A GLU* 3.7 2.5 - - - -
133A VAL* 4.7 0.9 - - - -
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Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 1.3 71.4 - - - +
96A GLU* 1.3 64.6 + - - +
98A TYR* 3.0 15.5 + - + +
99A ASN* 2.8 45.0 + - - +
132A GLU* 2.8 46.9 + - + +
133A VAL* 3.7 19.8 - - + +
137A GLU* 2.7 42.2 + - - -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 4.5 9.7 + - - +
94A SER* 3.2 9.0 + - - +
95A ARG* 1.3 79.2 - - - +
97A THR* 1.3 62.6 + - + +
99A ASN* 3.2 17.1 + - - +
100A ALA* 3.1 27.5 + - - +
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Residues in contact with THR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 3.9 22.4 + - + +
19A ALA 4.6 5.2 - - - +
20A GLY 5.8 0.4 - - - -
21A THR* 3.5 29.4 - - + -
89A VAL 5.1 0.9 - - - +
90A TYR* 3.6 9.5 - - - +
91A ASP* 2.9 26.7 + - + +
94A SER* 2.8 36.8 + - - +
96A GLU* 1.3 78.3 - - + +
98A TYR* 1.3 60.2 + - - +
100A ALA* 3.5 13.7 + - - +
101A LEU* 3.9 6.9 + - - +
104A TRP* 5.5 0.9 - - - -
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Residues in contact with TYR 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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90A TYR* 3.8 16.4 - + + -
94A SER 3.5 0.8 + - - +
95A ARG* 3.0 26.1 + - - +
97A THR* 1.3 75.8 + - - +
99A ASN* 1.3 78.8 + - - +
100A ALA 3.1 1.3 - - - -
101A LEU* 3.0 47.4 + - + +
102A THR 4.9 0.2 + - - -
120A LEU* 5.7 0.2 - - + -
133A VAL* 3.7 44.9 - - + -
137A GLU* 3.3 34.2 + - + +
138A ALA* 3.9 15.0 - - + -
141A PHE* 3.5 23.6 - + + +
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Residues in contact with ASN 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 ARG* 2.8 45.4 + - - +
96A GLU* 3.6 21.0 + - - +
98A TYR* 1.3 89.4 - - - +
100A ALA* 1.3 58.3 + - - +
101A LEU 3.1 1.5 + - - -
102A THR* 4.1 9.4 + - - -
103A ASN* 4.7 3.5 - - - +
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Residues in contact with ALA 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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18A ASN* 3.3 38.8 - - - +
96A GLU* 3.1 13.3 + - - +
97A THR 3.6 8.5 - - - +
98A TYR 3.1 1.0 - - - -
99A ASN* 1.3 76.4 - - - +
101A LEU* 1.3 64.5 + - - +
102A THR 3.2 0.7 - - - -
103A ASN* 3.0 26.2 + - + +
104A TRP* 3.3 17.2 + - - +
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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