Contacts of the strand formed by residues 174 - 179 (chain A) in PDB entry 5BPW
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 ASN 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 4.8 12.6 - - + +
75A PRO* 5.4 0.2 - - + -
115A TRP* 2.8 27.1 + - + +
116A MET* 3.2 17.5 - - - +
117A GLU* 4.0 12.1 - - + +
168A LEU 4.8 1.0 + - - -
171A VAL* 3.6 19.0 - - - +
172A ARG 3.3 13.1 + - - +
173A LEU* 1.3 76.6 - - - +
175A ILE* 1.3 64.0 + - - +
189A ALA* 3.6 1.4 - - - -
190A TYR* 2.7 59.1 + - - +
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Residues in contact with ILE 175 (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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114A HIS 3.7 0.5 - - - +
115A TRP* 3.6 4.0 - - - -
116A MET* 2.9 58.0 + - + +
173A LEU* 4.0 26.2 - - + -
174A ASN* 1.3 78.9 - - - +
176A LEU* 1.3 65.2 + - - +
177A VAL* 3.6 5.9 + - + +
187A LEU* 3.9 34.1 - - + -
188A TYR 3.6 10.8 - - - +
189A ALA* 4.5 4.0 - - - +
195A ILE* 4.3 17.9 - - + -
210A LEU* 4.2 7.9 - - + -
214A LEU* 4.3 11.0 - - + -
241A LEU* 4.5 7.0 - - + -
248A VAL* 6.5 0.2 - - + -
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Residues in contact with LEU 176 (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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72A ALA* 4.6 0.7 - - + -
81A ALA* 4.3 6.5 - - + -
90A ILE* 5.3 5.4 - - + -
92A LEU* 4.6 10.3 - - + -
104A PHE* 5.3 3.4 - - + -
113A MET* 3.7 35.2 - - + -
114A HIS 3.8 6.7 - - - +
115A TRP* 3.7 46.8 - - + +
175A ILE* 1.3 70.7 - - - +
177A VAL* 1.3 70.7 + - - +
178A LEU* 4.6 6.7 - - + -
188A TYR* 2.8 52.5 + - + +
191A GLY* 4.2 11.4 - - - +
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Residues in contact with VAL 177 (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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113A MET* 3.2 8.1 - - - +
114A HIS* 2.9 44.6 + - + +
116A MET* 5.3 0.2 - - + -
175A ILE* 4.2 5.4 - - + +
176A LEU* 1.3 75.4 - - - +
178A LEU* 1.3 64.9 + - - +
185A ILE* 3.9 12.6 - - + -
186A GLU 3.4 10.1 - - - +
187A LEU* 4.1 12.1 - - + +
208A LEU* 3.8 28.9 - - + +
210A LEU* 3.8 38.6 - - + -
217A LEU* 4.5 7.0 - - + -
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Residues in contact with LEU 178 (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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90A ILE* 3.6 30.7 - - + -
104A PHE* 4.7 3.8 - - + -
106A VAL* 3.9 14.6 - - + -
110A VAL* 3.7 11.7 - - + -
112A CYS 3.7 0.7 - - - -
113A MET* 3.5 35.0 - - + -
176A LEU* 4.4 6.1 - - + +
177A VAL* 1.3 78.3 - - - +
179A GLY* 1.3 59.3 + - - +
184A PHE 4.4 0.6 - - - +
185A ILE* 3.2 10.6 - - - +
186A GLU* 2.8 44.1 + - + +
188A TYR* 3.5 31.9 - - + -
208A LEU* 3.7 4.0 - - - -
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Residues in contact with GLY 179 (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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109A PRO 5.1 0.2 - - - -
110A VAL* 3.2 7.6 - - - +
111A SER* 2.7 28.5 + - - -
112A CYS 2.9 19.9 + - - -
178A LEU* 1.3 75.7 - - - +
180A GLY* 1.3 51.2 + - - -
184A PHE 4.3 6.5 - - - -
185A ILE* 4.4 0.9 - - - -
205A CYS* 4.1 9.6 - - - -
208A LEU* 3.6 15.4 - - - +
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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