Contacts of the strand formed by residues 19 - 24 (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 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B CYS 3.5 4.9 + - - +
18B ASP* 1.3 75.7 - - - +
20B VAL* 1.3 67.7 + - - +
59B THR* 3.6 20.6 - - + -
60B ARG 2.9 14.1 - - - +
62B LYS* 4.6 4.1 - - - +
119B CYS* 3.8 14.6 - - + +
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Residues in contact with VAL 20 (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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19B ALA* 1.3 78.6 - - - +
21B SER* 1.3 64.5 + - - +
58B GLU 3.6 1.4 - - - +
59B THR* 3.3 2.3 - - - -
60B ARG* 2.8 41.1 + - + +
61B CYS 3.9 15.7 - - - +
62B LYS* 4.0 22.9 - - + -
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Residues in contact with SER 21 (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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19B ALA 5.5 0.2 - - - -
20B VAL* 1.3 76.6 - - - +
22B GLY* 1.3 59.1 + - - +
57B PHE* 3.7 22.2 - - - -
58B GLU 3.4 3.6 - - - -
59B THR* 2.9 29.1 + - - +
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Residues in contact with GLY 22 (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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21B SER* 1.3 79.0 - - - +
23B TRP* 1.3 70.0 + - - -
24B VAL* 3.8 3.5 + - - +
57B PHE* 3.5 17.2 - - - -
58B GLU 3.1 31.0 + - - +
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Residues in contact with TRP 23 (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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31A MET* 3.5 41.3 - - + -
102A PHE* 3.3 46.2 - + - -
22B GLY* 1.3 74.5 - - - -
24B VAL* 1.3 61.5 + - - +
25B THR* 3.9 14.2 + - + +
55B TYR* 3.6 18.8 - + + -
56B PHE 3.5 17.7 - - - -
57B PHE* 3.8 24.9 - + + -
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Residues in contact with VAL 24 (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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22B GLY 4.5 3.8 - - - +
23B TRP* 1.3 76.4 - - - +
25B THR* 1.3 60.7 + - - +
26B ASP* 3.6 20.6 - - - +
27B ARG* 3.6 27.5 + - + +
55B TYR* 3.4 7.4 - - - +
56B PHE* 3.1 32.7 + - + +
58B GLU* 3.8 27.6 - - + +
60B ARG* 3.7 33.7 - - - +
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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