Contacts of the strand formed by residues 175 - 181 (chain A) in PDB entry 1B54
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 ILE 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ALA* 3.3 32.1 - - - +
123A LEU* 3.8 31.4 - - + +
124A ASN* 3.8 18.4 - - + +
127A ARG* 4.8 0.2 - - + -
136A PRO* 4.3 2.0 - - - -
137A ILE* 3.2 19.7 - - + +
139A CYS* 3.9 8.7 - - - -
166A PHE* 4.3 0.4 - - + -
167A PHE* 3.6 26.3 - - + +
172A CYS* 3.3 37.2 - - - +
173A LYS 3.7 0.9 - - - -
174A TYR* 1.3 84.8 + - - +
176A LYS* 1.3 61.1 + - - +
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Residues in contact with LYS 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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135A ASN* 5.5 2.4 - - - +
136A PRO* 4.3 29.8 + - + +
137A ILE 2.7 9.1 + - - +
138A LEU* 3.4 30.7 - - + +
139A CYS 2.6 33.6 + - - -
167A PHE* 4.0 2.9 - - - -
175A ILE* 1.3 73.4 - - - +
177A LEU* 1.3 68.2 + - - +
178A ASN* 4.4 0.4 - - - -
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Residues in contact with LEU 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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139A CYS 3.7 4.9 - - - +
141A VAL* 3.8 18.2 - - + -
164A ILE* 3.6 47.6 - - + -
167A PHE* 3.4 36.2 + - + -
168A LEU* 4.0 20.0 - - + -
176A LYS* 1.3 80.5 - - - +
178A ASN* 1.3 62.0 + - - +
179A GLY 4.1 10.8 - - - +
215A THR* 4.4 3.8 - - + -
217A LEU* 4.0 21.6 - - + +
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Residues in contact with ASN 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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138A LEU* 4.0 30.6 - - + +
139A CYS 2.6 25.5 + - - +
140A ASN* 3.3 14.2 + - - +
176A LYS* 3.3 0.8 + - - +
177A LEU* 1.3 75.8 - - - +
179A GLY* 1.3 57.8 + - - +
216A SER 5.0 0.9 - - - +
217A LEU* 3.9 8.5 - - - +
218A LYS* 3.0 56.9 + - - +
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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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139A CYS 4.1 0.3 - - - +
140A ASN* 2.7 17.3 - - - +
141A VAL* 2.8 23.0 + - - +
177A LEU* 3.9 4.9 - - - +
178A ASN* 1.3 78.4 - - - +
180A LEU* 1.3 68.8 + - - +
217A LEU* 3.7 8.9 - - - +
218A LYS 2.7 19.1 - - - -
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Residues in contact with LEU 180 (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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140A ASN* 4.2 2.1 - - - -
141A VAL* 3.4 19.1 - - + +
143A ILE* 3.9 15.0 - - + -
164A ILE* 4.9 1.8 - - + -
179A GLY* 1.3 81.8 - - - +
181A MET* 1.3 62.3 + - - +
202A LEU* 3.8 13.9 - - + +
205A TRP* 3.9 15.7 - - + -
206A LYS* 3.6 40.4 - - + +
209A ILE* 4.2 12.8 - - + -
217A LEU* 3.4 24.2 - - + +
218A LYS 2.8 5.7 + - - +
219A LEU* 3.8 12.8 - - + -
220A SER* 2.9 28.2 + - - -
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Residues in contact with MET 181 (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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91A ILE* 4.2 2.7 - - + +
112A GLU* 3.3 35.7 - - + +
113A THR* 3.6 30.7 - - + -
140A ASN* 3.9 8.3 - - + -
141A VAL 2.8 10.3 + - - +
142A GLN* 3.3 15.9 - - + -
143A ILE* 2.8 31.2 + - - +
180A LEU* 1.3 78.3 - - - +
182A THR* 1.3 92.7 + - - +
183A ILE* 4.1 2.9 - - + -
202A LEU* 4.5 3.4 - - - -
220A SER* 3.4 13.2 - - - +
239A ARG* 3.8 14.6 - - - +
258A PLP 3.8 26.0 - - + -
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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
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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