Contacts of the strand formed by residues 118 - 125 (chain B) in PDB entry 1B8M
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 ALA 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A THR* 5.2 0.2 - - - +
108A SER* 3.3 31.2 - - - +
110A VAL* 4.5 4.9 - - + -
59B THR* 3.2 20.6 + - - +
92B ALA* 3.1 9.7 - - - +
93B LYS* 2.8 40.0 + - + -
117B THR* 1.3 82.8 - - - +
119B CYS* 1.3 59.6 + - - +
120B VAL* 4.0 6.3 - - + -
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Residues in contact with CYS 119 (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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110A VAL* 4.4 10.1 - - - +
17B CYS* 3.6 34.1 - - + +
18B ASP 3.9 4.9 - - - -
19B ALA* 3.8 14.0 - - + +
59B THR* 4.7 2.4 - - - +
60B ARG 3.7 15.7 - - - +
61B CYS* 2.0 49.4 - - - -
90B CYS* 3.9 7.4 - - - -
91B LYS 3.4 3.4 - - - -
118B ALA* 1.3 75.1 - - - +
120B VAL* 1.3 61.3 + - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 6.0 1.6 - - - +
11A SER* 4.4 12.6 - - - +
12A VAL* 5.8 2.2 - - + -
108A SER* 5.2 2.2 - - - -
109A CYS 4.7 7.4 - - - +
110A VAL* 4.3 21.1 - - + -
17B CYS* 3.7 5.4 - - - -
90B CYS* 3.3 1.6 - - - -
91B LYS* 2.8 44.5 + - + +
92B ALA 5.1 0.9 - - - +
93B LYS* 4.1 45.8 - - + -
118B ALA* 4.3 4.5 - - + -
119B CYS* 1.3 79.4 - - - +
121B CYS* 1.3 65.6 + - - +
122B THR* 3.7 6.9 + - - +
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Residues in contact with CYS 121 (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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11A SER* 3.4 7.6 + - - -
12A VAL* 3.1 45.2 + - + +
16B VAL* 3.9 8.7 - - + -
17B CYS* 3.6 7.6 - - - -
78B CYS* 2.0 54.5 - - + -
81B VAL* 4.1 12.6 - - - -
88B SER* 4.1 8.3 - - - -
89B GLU 3.9 0.2 - - - -
120B VAL* 1.3 74.1 - - - +
122B THR* 1.3 64.1 + - - +
123B LEU* 4.4 4.9 - - - -
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Residues in contact with THR 122 (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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9A GLU* 4.4 14.4 + - + +
10A LEU 3.4 18.8 - - - +
11A SER* 4.6 1.4 + - - +
88B SER* 3.1 6.6 - - - -
89B GLU* 2.7 44.2 + - - +
91B LYS* 3.8 35.2 - - - +
120B VAL* 4.1 6.6 + - - +
121B CYS* 1.3 76.1 + - - +
123B LEU* 1.3 73.3 + - - +
124B LEU* 3.6 12.7 + - + -
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Residues in contact with LEU 123 (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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10A LEU* 2.8 44.8 + - + +
12A VAL* 4.9 8.7 - - + +
69A ARG* 4.2 27.1 - - + +
70A GLY* 4.4 4.0 - - - -
81B VAL* 4.5 11.0 - - + -
86B TRP* 3.8 56.2 - - + -
87B VAL 3.7 1.1 - - - -
88B SER* 4.1 15.5 - - - -
121B CYS* 4.4 9.2 - - - -
122B THR* 1.3 83.0 - - - +
124B LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 124 (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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86B TRP* 5.4 0.4 - - - -
87B VAL* 2.6 37.4 + - + +
88B SER 4.4 1.8 - - - +
89B GLU* 3.9 31.0 - - + +
91B LYS* 4.4 13.7 - - - +
122B THR* 3.6 21.3 + - + +
123B LEU* 1.3 75.8 - - - +
125B SER* 1.3 62.0 + - - +
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Residues in contact with SER 125 (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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86B TRP* 3.3 19.7 - - - -
87B VAL* 3.2 37.5 + - - +
123B LEU 3.8 1.0 - - - -
124B LEU* 1.3 81.1 - - - +
126B ARG* 1.3 76.1 + - - +
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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