Contacts of the strand formed by residues 155 - 159 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ASP* 2.8 42.7 + - - +
146C LEU* 3.5 31.9 - - + -
147C LYS* 3.5 32.6 - - - +
152C PHE* 2.5 41.2 + - + +
153C LYS* 3.7 16.6 + - - +
154C HIS* 1.3 79.0 - - - +
156C LEU* 1.3 61.7 + - - +
157C TRP* 4.0 2.5 + - - +
167C CYS* 4.4 9.9 - - - -
168C TRP 3.6 4.0 - - - -
169C VAL* 4.3 13.2 - - + -
336C LEU* 4.1 22.8 - - - +
398C PHE* 4.1 9.2 - - - +
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Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TRP* 4.7 10.3 - - + -
155C ARG* 1.3 72.3 - - - +
157C TRP* 1.3 63.4 + - - +
158C VAL* 4.0 17.9 - - + -
167C CYS* 3.4 2.2 - - - -
168C TRP* 2.7 49.2 + - + +
320C PRO* 4.4 13.0 - - + -
333C PRO* 4.2 20.0 - - + -
334C ILE 6.0 0.4 - - - +
394C VAL* 5.2 3.4 - - + +
395C PHE* 3.7 32.8 - - + -
398C PHE* 3.8 43.9 - - + -
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Residues in contact with TRP 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PHE* 5.3 2.2 - - + -
110C ILE* 3.9 17.0 - - + -
139C ILE* 3.6 36.8 - - + -
142C ILE* 3.8 30.5 - - + -
143C ASP* 2.8 41.6 + - + +
146C LEU* 4.8 0.2 - - + -
155C ARG* 4.0 4.2 + - - +
156C LEU* 1.3 73.7 - - - +
158C VAL* 1.3 62.8 + - - +
165C VAL* 3.7 23.1 - - + -
166C HIS 3.4 20.0 - - - -
167C CYS* 3.6 34.6 - - + -
333C PRO* 3.4 6.6 - - - +
334C ILE* 2.8 46.0 + - + +
336C LEU* 3.7 20.2 - - + +
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Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 4.0 15.7 - - + -
157C TRP* 1.3 80.8 - - - +
159C TYR* 1.3 66.5 + - - +
165C VAL* 3.2 2.6 - - - -
166C HIS* 2.6 52.2 + - + +
168C TRP* 3.9 25.8 - - + +
320C PRO* 4.0 18.8 - - + -
331C SER* 3.4 35.0 - - - +
332C VAL 3.5 9.2 - - - +
333C PRO* 4.2 3.6 - - + -
334C ILE* 4.0 4.3 - - - -
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Residues in contact with TYR 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 3.9 4.0 - - - +
132C TRP* 3.4 35.0 - + - -
158C VAL* 1.3 72.3 - - - +
160C SER* 1.3 57.2 + - - +
161C GLY* 3.3 32.1 + - - -
162C ARG* 3.2 28.0 + - - -
164C GLY 3.3 17.9 - - - -
165C VAL* 4.3 0.2 - - - -
329C ARG* 4.3 11.1 + - + +
330C ILE 4.2 9.2 - - - -
331C SER* 3.1 28.8 + - - -
332C VAL* 2.9 14.6 + - + +
334C ILE* 3.7 7.5 - - + +
342C PHE* 3.6 24.2 - + + -
344C PRO* 3.6 30.1 + - + +
347C VAL* 4.1 15.0 - - + -
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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
------------------------------------------------------------
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