Contacts of the helix formed by residues 95 - 103 (chain A) in PDB entry 2B7O
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 THR 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A MSE 3.6 21.3 - - - +
93A ASP* 2.9 9.5 + - - -
94A ASN* 1.3 77.6 - - - +
96A GLU* 1.3 66.0 + - - +
97A PRO* 3.4 13.0 - - - +
98A HIS* 3.3 21.0 + - - +
99A ILE* 3.0 28.8 + - - +
1001A CE1 4.1 8.3 - - - +
54B SER* 3.8 22.7 - - - +
56B PRO* 4.6 2.2 - - - -
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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
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95A THR* 1.3 71.3 - - - +
97A PRO* 1.4 77.8 - - + +
100A ARG* 2.5 80.1 + - - +
182A LEU* 3.6 27.9 - - + +
186A LEU* 4.6 6.9 - - - +
54B SER 5.0 1.0 + - - -
55B VAL 5.0 1.7 + - - +
56B PRO* 4.5 6.2 - - + +
57B PRO* 3.9 25.4 - - + -
60B VAL* 5.8 2.0 - - + +
260B ARG* 6.0 3.1 - - - +
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Residues in contact with PRO 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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95A THR* 3.4 14.1 - - - +
96A GLU* 1.4 103.8 - - + +
98A HIS* 1.3 56.7 + - - +
100A ARG* 3.9 16.9 + - - +
101A GLY* 3.1 23.4 + - - -
415A GLU* 4.0 9.0 - - - +
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Residues in contact with HIS 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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86A ASP* 2.5 42.3 + - - -
93A ASP* 3.0 48.5 - - + +
94A ASN* 5.2 0.4 - - - -
95A THR* 3.2 9.9 + - - +
97A PRO* 1.3 77.5 - - - +
99A ILE* 1.3 70.9 + - + +
101A GLY* 3.3 1.9 + - - -
102A ASN* 3.1 33.5 + - - +
413A THR* 3.6 17.0 + - - -
415A GLU* 2.9 28.7 + - - +
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Residues in contact with ILE 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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89A GLU* 5.9 0.2 - - - +
94A ASN* 3.4 26.9 - - - +
95A THR 3.0 22.0 + - - +
96A GLU 4.0 2.0 - - - +
98A HIS* 1.3 82.1 - - + +
100A ARG* 1.3 57.7 + - - +
102A ASN* 3.3 6.3 + - - +
103A VAL* 2.9 41.3 + - + +
127A ILE* 4.2 13.0 - - + -
179A ALA* 3.7 22.4 - - + -
182A LEU* 3.9 24.2 - - + -
183A VAL* 4.2 16.4 - - + -
186A LEU* 4.3 1.6 - - + -
56B PRO* 3.9 16.4 - - + -
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Residues in contact with ARG 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 GLU* 2.5 59.2 + - - +
97A PRO* 3.9 19.3 + - - +
99A ILE* 1.3 77.7 - - - +
101A GLY* 1.3 56.7 + - - +
103A VAL* 3.2 1.9 + - - +
104A ARG* 2.8 32.2 + - + +
186A LEU* 3.7 23.7 - - + +
191A LEU* 4.3 28.5 - - + -
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Residues in contact with GLY 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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97A PRO 3.1 16.5 + - - -
98A HIS 3.3 3.3 + - - -
99A ILE 3.3 0.2 - - - -
100A ARG* 1.3 78.0 - - - +
102A ASN* 1.3 59.3 + - - +
104A ARG* 3.8 6.0 - - - +
105A ALA* 3.0 27.9 + - - +
414A GLY* 3.6 20.9 - - - -
415A GLU* 5.3 2.5 - - - -
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Residues in contact with ASN 102 (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 GLY* 4.9 7.8 - - - -
86A ASP* 3.1 34.5 + - - +
98A HIS* 3.1 29.4 + - - +
99A ILE* 3.8 4.9 - - - +
101A GLY* 1.3 73.3 - - - +
103A VAL* 1.3 65.0 - - - +
105A ALA* 3.8 5.1 - - - +
106A LEU* 3.1 25.1 + - - +
126A ARG 5.7 0.6 + - - -
127A ILE* 4.9 16.3 - - + +
412A ILE* 4.7 6.7 - - + +
413A THR* 3.5 12.4 + - - -
414A GLY 3.1 21.0 + - - -
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Residues in contact with VAL 103 (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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99A ILE* 2.9 25.1 + - + +
100A ARG 3.6 4.5 - - - +
102A ASN* 1.3 73.1 - - - +
104A ARG* 1.3 66.4 + - - +
106A LEU* 3.3 5.2 + - - +
107A LEU* 3.0 30.2 + - + +
127A ILE* 5.0 4.9 - - + -
183A VAL* 4.1 24.0 - - + -
186A LEU* 4.1 21.3 - - + -
187A THR* 4.5 3.4 - - + -
191A LEU* 3.6 22.9 - - + -
243A ILE* 3.8 26.8 - - + +
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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