Contacts of the strand formed by residues 155 - 159 (chain A) in PDB entry 4BPW
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 ARG 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASP* 2.6 44.0 + - - +
146A LEU* 3.7 28.3 - - - -
147A LYS* 3.6 30.5 - - - +
152A PHE* 2.7 40.5 + - + +
153A LYS* 3.7 19.0 + - - +
154A HIS* 1.3 79.4 - - - +
156A LEU* 1.3 60.8 + - - +
157A TRP* 3.9 6.3 + - - +
167A CYS* 4.3 10.5 - - - -
168A TRP 3.3 4.9 - - - +
169A VAL* 4.1 13.0 - - + -
336A LEU* 3.9 19.6 - - - +
398A PHE* 4.0 9.0 - - - +
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP* 4.6 5.8 - - + -
154A HIS 4.2 0.4 - - - -
155A ARG* 1.3 71.9 - - - +
157A TRP* 1.3 63.1 + - - +
158A VAL* 3.8 18.8 - - + -
167A CYS* 3.3 1.7 - - - -
168A TRP* 2.7 52.9 + - + +
320A PRO* 4.1 16.6 - - + -
333A PRO* 3.9 26.0 - - + -
334A ILE 5.5 0.7 - - - +
394A VAL* 5.2 4.0 - - + +
395A PHE* 3.7 37.7 - - + -
398A PHE* 4.1 29.4 - - + -
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Residues in contact with TRP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 5.4 1.1 - - + -
110A ILE* 4.0 14.1 - - + -
139A ILE* 3.6 34.8 - - + -
142A ILE* 3.8 31.9 - - + -
143A ASP* 3.1 34.2 + - + +
155A ARG 3.9 4.4 + - - -
156A LEU* 1.3 72.7 - - - +
158A VAL* 1.3 58.8 + - - +
165A VAL* 3.6 22.9 - - + -
166A HIS 3.3 18.8 - - - -
167A CYS* 3.3 35.7 - - + -
333A PRO* 3.3 7.3 - - - +
334A ILE* 2.7 53.5 + - + +
336A LEU* 3.6 28.2 - - + +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 3.8 24.7 - - + -
157A TRP* 1.3 80.6 - - - +
159A TYR* 1.3 73.5 + - - +
160A SER* 5.6 0.2 - - - -
165A VAL* 3.1 3.5 - - - -
166A HIS* 2.6 48.7 + - + +
168A TRP* 3.8 23.1 - - + +
318A LYS 6.2 0.2 - - - +
319A SER 5.8 0.2 - - - -
320A PRO* 4.2 12.8 - - + -
331A SER* 3.5 24.7 - - - +
332A VAL 3.5 14.1 - - - +
333A PRO* 4.7 1.8 - - + -
334A ILE* 3.8 5.3 - - - +
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ILE* 4.2 2.9 - - - +
132A TRP* 3.7 19.3 - + - -
158A VAL* 1.3 72.5 - - - +
160A SER* 1.3 58.9 + - - +
161A GLY* 3.3 34.2 + - - -
162A ARG* 3.2 29.2 + - - -
164A GLY 3.3 16.4 - - - -
329A ARG* 4.0 13.8 + - + +
330A ILE 4.0 11.7 - - - -
331A SER* 3.2 28.6 + - - -
332A VAL* 3.0 16.7 + - + +
334A ILE* 3.6 7.0 - - - +
342A PHE* 3.5 26.0 - + + -
344A PRO* 3.5 38.4 + - + +
347A VAL* 4.1 12.1 - - + -
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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