Contacts of the strand formed by residues 157 - 164 (chain B) in PDB entry 3A4T
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 PHE 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.3 40.2 - + - +
87B ILE 3.4 31.2 - - - -
88B LEU* 3.5 31.9 - - + -
112B VAL* 3.9 15.9 - - + -
150B LEU* 4.3 16.2 - - + -
155B ILE* 3.9 20.6 - - + -
156B PHE* 1.3 79.6 - - - +
158B ASP* 1.3 66.0 + - - +
159B LYS 3.8 11.7 - - - +
160B ILE* 3.8 13.7 - - + -
200B LEU* 2.9 19.5 + - + +
201B LEU* 3.8 4.0 - - - +
202B LYS* 2.9 25.7 + - - +
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Residues in contact with ASP 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 ARG* 4.1 12.2 + - - +
84B ASP 4.8 0.7 - - - +
85B ASP* 3.5 29.6 - - - +
86B PHE* 2.8 42.0 + - - +
157B PHE* 1.3 73.6 - - - +
159B LYS* 1.3 67.1 + - - +
201B LEU* 4.6 0.2 - - - -
202B LYS* 2.8 36.0 + - - +
205B GLY* 3.1 24.7 - - - -
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Residues in contact with LYS 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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79B LEU* 3.3 28.3 - - + +
80B ASN* 3.4 11.2 + - - +
81B PRO* 4.1 5.2 - - + -
82B ARG* 3.1 36.5 - - - +
85B ASP* 3.5 16.4 - - - +
86B PHE 3.6 2.8 + - - -
87B ILE* 3.3 20.6 - - + +
88B LEU 3.1 21.8 + - - -
157B PHE* 3.8 1.2 - - - +
158B ASP* 1.3 89.8 - - + +
160B ILE* 1.3 67.7 + - - +
201B LEU* 4.2 0.2 - - - -
206B GLU* 2.8 46.9 + - - +
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Residues in contact with ILE 160 (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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79B LEU* 3.4 7.7 - - - +
88B LEU* 3.4 23.6 - - + +
90B MET* 3.7 29.8 - - + -
157B PHE* 3.8 9.6 - - + -
159B LYS* 1.3 82.1 - - - +
161B LEU* 1.3 64.6 - - - +
197B GLY* 3.3 25.1 - - - +
200B LEU* 3.7 31.0 - - + +
201B LEU* 3.5 11.2 - - + -
206B GLU 2.9 8.7 + - - -
207B LEU* 3.3 18.2 - - + +
208B VAL 3.0 25.5 + - - +
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Residues in contact with LEU 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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75B PRO* 4.1 17.0 - - + -
76B PRO* 5.1 4.3 - - + -
79B LEU* 4.1 16.2 - - + +
87B ILE* 4.9 0.2 - - - +
88B LEU 2.7 13.3 + - - +
89B ASP* 3.5 18.9 - - - +
90B MET* 3.0 28.9 + - - +
97B LYS* 3.5 33.0 - - + -
101B LEU* 3.9 23.6 - - + -
160B ILE* 1.3 73.8 - - - +
162B LEU* 1.3 61.2 + - - +
163B ASP* 3.4 33.8 + - + +
208B VAL* 3.8 9.9 - - + +
210B SER* 4.0 9.0 - - - +
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Residues in contact with LEU 162 (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* 3.9 19.3 - - + -
91B CYS* 4.2 8.1 - - - -
160B ILE* 3.8 3.4 - - - +
161B LEU* 1.3 69.7 - - - +
163B ASP* 1.3 61.6 + - - +
164B ALA* 3.3 30.0 + - + +
193B LEU* 3.5 23.1 - - + +
194B ILE* 3.2 52.5 - - + +
207B LEU* 4.6 8.1 - - + -
208B VAL 2.8 16.0 + - - +
209B TYR* 3.5 12.8 - - + -
210B SER 2.9 26.3 + - - +
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Residues in contact with ASP 163 (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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89B ASP* 5.0 1.6 + - - -
91B CYS* 3.5 27.1 - - - +
97B LYS* 2.6 36.0 + - + -
161B LEU* 3.4 22.0 + - + +
162B LEU* 1.3 72.2 - - - +
164B ALA* 1.3 65.1 + - - +
210B SER* 2.7 34.8 + - - +
211B THR* 4.1 2.9 + - - -
212B CYS* 5.0 1.2 + - - -
266B PHE* 3.9 7.4 - - - -
501B SFG 2.9 35.3 + - - +
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Residues in contact with ALA 164 (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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91B CYS* 4.3 0.4 - - - -
162B LEU* 3.3 23.4 + - + -
163B ASP* 1.3 79.0 - - - +
165B PRO* 1.4 69.2 - - + +
166B CYS 3.8 0.3 + - - -
190B GLN* 3.7 28.9 - - + -
193B LEU* 5.2 1.1 - - + -
209B TYR* 3.8 7.4 - - + +
210B SER 2.9 12.7 + - - +
211B THR* 3.0 20.6 + - - +
212B CYS* 4.4 2.3 - - - -
501B SFG 4.1 7.5 + - - -
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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