Contacts of the strand formed by residues 155 - 161 (chain B) in PDB entry 6A5T
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 LYS 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B TYR* 3.6 37.7 - - + +
116B TYR* 4.2 30.3 - - + -
117B LEU 3.1 6.7 - - - +
118B ASP* 3.8 13.6 + - - +
154B ASN* 1.3 90.4 + - - +
156B VAL* 1.3 61.7 + - - +
157B HIS 4.1 0.9 + - - -
438B ASN* 4.3 10.9 + - - -
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Residues in contact with VAL 156 (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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116B TYR* 3.4 5.6 - - - -
117B LEU 2.5 37.8 + - - +
119B MET* 3.7 20.6 - - + -
153B GLY 5.8 0.2 - - - +
154B ASN 3.6 10.5 - - - +
155B LYS* 1.3 78.3 - - - +
157B HIS* 1.3 75.3 + - - +
158B ILE* 3.1 16.1 - - + +
437B LEU* 3.1 30.3 - - + +
438B ASN* 4.7 9.6 - - - +
441B VAL* 3.6 27.6 - - + -
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Residues in contact with HIS 157 (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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114B PRO* 3.8 32.1 - - + +
115B VAL 4.2 0.4 - - - -
116B TYR* 3.3 31.2 - + + +
155B LYS 4.1 0.8 + - - -
156B VAL* 1.3 82.8 - - - +
158B ILE* 1.3 59.0 + - - +
159B GLY* 4.4 7.6 + - - -
160B LYS* 4.2 21.5 - - + +
441B VAL* 4.1 3.3 - - - +
443B SER* 3.5 30.2 + - - -
447B THR* 5.9 0.7 - - - -
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Residues in contact with ILE 158 (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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82B ILE* 6.3 0.7 - - + -
115B VAL* 3.5 24.1 + - + +
117B LEU* 3.4 40.4 - - + -
119B MET* 5.2 0.4 - - - -
156B VAL* 3.1 28.5 + - + +
157B HIS* 1.3 75.1 - - - +
159B GLY* 1.3 62.7 + - - +
410B PHE* 5.2 6.3 - - + -
414B PHE* 5.2 5.8 - - + -
417B LEU* 4.8 7.3 - - + +
441B VAL* 3.9 14.4 - - + +
443B SER* 3.3 27.0 - - - +
446B ILE* 3.8 33.2 - - + +
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Residues in contact with GLY 159 (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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114B PRO* 3.5 3.5 - - - +
115B VAL* 2.9 33.0 + - - +
157B HIS* 3.9 5.8 + - - -
158B ILE* 1.3 84.8 - - - +
160B LYS* 1.3 65.4 + - - -
161B VAL* 4.0 1.1 - - - -
443B SER* 4.0 5.2 - - - -
446B ILE* 4.4 10.5 - - - -
447B THR* 3.7 11.9 - - - -
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR 4.8 10.0 + - - -
90B THR* 5.9 5.5 - - - +
112B SER* 3.0 32.0 + - - +
113B SER 3.2 10.8 - - - +
114B PRO* 4.3 13.7 - - + -
157B HIS* 4.2 20.6 - - + +
159B GLY* 1.3 78.3 - - - +
161B VAL* 1.3 64.0 + - - +
162B PRO* 3.2 13.2 - - - +
446B ILE* 4.9 3.6 - - - +
447B THR* 3.4 31.6 + - + +
450B LEU* 4.6 11.0 - - - +
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Residues in contact with VAL 161 (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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38B PHE* 5.1 0.9 - - + -
41B PHE* 4.2 9.9 - - + -
42B MET* 3.4 38.1 - - + -
46B ILE* 4.1 20.2 - - + -
84B LEU* 6.2 0.2 - - + -
113B SER* 2.8 31.3 + - - +
115B VAL* 3.7 21.6 - - + +
160B LYS* 1.3 70.7 - - - +
162B PRO* 1.3 74.3 - - + +
163B ILE* 3.6 0.7 + - - +
406B LEU* 5.2 3.4 - - + -
410B PHE* 4.3 18.4 - - + -
446B ILE* 5.9 0.7 - - + -
450B LEU* 4.9 6.5 - - + -
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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