Contacts of the helix formed by residues 96 - 103 (chain B) in PDB entry 5B2S
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 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B ASP* 3.1 3.4 + - - -
95B ASP* 1.3 85.3 + - - +
97B PHE* 1.3 65.7 + - - +
98B PHE 3.4 2.5 - - - -
99B HIS* 3.1 10.9 + - - +
100B ARG* 2.9 43.7 + - - +
113B HIS* 3.7 34.1 + - - +
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B MET* 3.8 22.0 - - + -
94B ASP* 3.2 28.0 + - + +
95B ASP 3.7 0.4 - - - -
96B SER* 1.3 76.1 - - - +
98B PHE* 1.3 82.9 + + - +
100B ARG* 3.2 16.0 + - - +
101B LEU* 3.2 36.2 + - + +
117B PRO 4.0 1.6 - - - -
118B ILE* 3.5 30.7 - - + -
152B ARG* 3.6 33.7 - - + -
155B TYR* 3.7 22.0 - + - -
156B LEU* 3.9 22.0 - - + -
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Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLN* 3.7 52.1 + - + +
86B PHE* 3.8 23.8 - - + -
87B SER* 4.5 6.1 - - - -
90B MET* 4.0 29.6 - - + +
96B SER 3.4 0.6 - - - -
97B PHE* 1.3 102.7 - + - +
99B HIS* 1.3 66.7 + - + +
101B LEU* 3.4 6.8 + - + +
102B GLU* 3.2 27.6 + - + +
155B TYR* 3.8 24.5 - + - -
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Residues in contact with HIS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP 3.8 13.4 + - - -
96B SER* 3.1 21.4 + - - +
98B PHE* 1.3 79.9 - - + +
100B ARG* 1.3 64.9 + - - +
102B GLU* 3.2 8.5 + - + +
103B GLU* 3.2 26.9 + - - +
113B HIS* 3.6 30.4 + + + +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASP* 2.7 33.7 + - - -
96B SER* 2.9 38.4 + - - +
97B PHE* 3.6 15.3 - - - +
99B HIS* 1.3 75.9 - - - +
101B LEU* 1.3 63.0 + - - +
103B GLU* 3.7 10.0 - - - +
104B SER* 3.2 22.5 + - - -
111B LYS* 5.4 0.3 + - - -
113B HIS* 3.8 22.9 - - + -
114B GLU* 3.5 23.8 - - - +
116B HIS 3.4 10.4 + - - -
117B PRO* 2.6 33.9 + - + +
118B ILE 2.9 26.3 + - - -
119B PHE 3.9 2.8 + - - +
120B GLY* 4.0 14.4 - - - -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A A 2.6 46.0 + - - +
48A A 3.6 9.1 - - - +
83B GLN* 4.6 5.4 - - - +
97B PHE* 3.2 38.7 + - + +
98B PHE* 3.7 15.5 - - + +
99B HIS 3.2 0.8 - - - -
100B ARG* 1.3 77.7 - - - +
102B GLU* 1.3 62.4 + - + +
104B SER* 3.2 9.1 + - - -
117B PRO* 4.2 21.3 - - + +
118B ILE* 5.4 1.8 - - + -
155B TYR* 3.6 32.5 - - + +
156B LEU* 4.0 15.0 - - + -
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A A 4.2 30.1 + - - +
49A A 4.9 0.2 + - - -
76B LYS* 2.9 31.4 + - - -
79B ILE* 5.9 0.3 - - - +
80B LEU* 5.1 3.0 - - - +
83B GLN* 4.5 18.8 + - - +
98B PHE 3.2 17.4 + - - +
99B HIS* 3.2 12.0 + - + +
101B LEU* 1.3 77.6 - - + +
103B GLU* 1.3 58.1 + - + +
104B SER 3.4 1.3 + - - -
105B PHE* 4.8 2.9 + - - +
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B HIS 3.2 14.2 + - - +
100B ARG* 3.9 8.7 - - - +
101B LEU 3.3 0.2 - - - -
102B GLU* 1.3 75.0 - - + +
104B SER* 1.3 61.2 + - - +
105B PHE* 3.1 4.6 + - - -
106B LEU* 3.1 30.8 + - + +
111B LYS* 2.8 35.1 + - + +
112B LYS* 2.9 30.0 + - - +
113B HIS* 2.9 43.7 + - - +
114B GLU 4.8 1.0 - - - +
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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