Contacts of the strand formed by residues 180 - 186 (chain A) in PDB entry 5B4N
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ASP* 3.1 34.0 + - + +
150A TRP* 3.4 13.9 + - - -
178A THR 3.4 7.6 - - - +
179A CYS* 1.3 78.7 - - - +
181A LYS* 1.3 63.6 + - - +
221A GLN* 3.2 43.6 + - - +
223A THR* 4.2 8.1 + - - -
272A GLU* 2.8 42.5 + - + +
273A HIS* 3.2 23.6 - - - +
274A GLY 3.3 7.5 + - - +
275A GLY 2.6 36.3 + - - +
277A ASP* 4.5 16.6 - - - +
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Residues in contact with LYS 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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137A LEU* 5.9 0.9 - - + -
140A TRP* 3.4 47.2 - - + -
141A SER 3.3 13.9 - - - +
142A LEU* 4.1 11.9 - - + -
143A ASP 5.2 0.2 - - - +
150A TRP* 3.7 31.4 - - + +
172A PHE* 3.6 40.8 - - + -
180A ARG* 1.3 76.2 - - - +
182A ALA* 1.3 62.7 + - - +
272A GLU* 3.5 3.9 - - - +
273A HIS* 2.9 64.7 + - - +
289A VAL* 4.0 1.3 - - - -
292A SER* 5.0 0.4 + - - -
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TRP* 3.6 7.8 - - - -
141A SER* 2.9 40.9 + - - +
181A LYS* 1.3 79.9 - - - +
183A GLN* 1.3 64.3 + - - +
270A ARG* 3.6 32.8 - - - +
271A PHE 3.2 8.3 - - - +
272A GLU* 3.6 11.9 - - + -
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Residues in contact with GLN 183 (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 LEU 4.3 2.3 - - - +
128A LEU* 3.5 23.8 - - + +
129A ARG* 2.6 52.5 + - - +
139A GLY 3.5 24.0 + - - +
140A TRP* 3.6 24.2 - - + -
141A SER* 5.0 2.9 - - - -
182A ALA* 1.3 76.6 - - - +
184A VAL* 1.3 73.2 + - - +
185A ILE* 4.2 2.1 - - + +
269A VAL 3.8 0.7 - - - +
270A ARG* 3.5 2.5 - - - +
271A PHE* 2.8 33.3 + - - +
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Residues in contact with VAL 184 (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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183A GLN* 1.3 84.4 - - - +
185A ILE* 1.3 64.3 + - - +
186A ASP 4.1 1.0 + - - -
227A LEU* 5.1 4.7 - - + -
268A PHE* 3.9 35.7 - - + -
269A VAL 3.4 5.6 - - - +
270A ARG* 3.8 34.3 - - + +
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Residues in contact with ILE 185 (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 LEU* 3.8 44.9 - - + +
128A LEU* 3.6 31.4 - - + -
183A GLN* 4.9 3.8 - - - +
184A VAL* 1.3 73.9 - - - +
186A ASP* 1.3 71.6 + - - +
187A LEU* 3.7 10.3 + - + -
190A GLU* 4.3 4.9 - - + +
268A PHE* 3.1 13.1 - - - -
269A VAL* 2.8 45.2 + - + +
271A PHE* 5.2 1.3 - - + -
294A VAL* 3.6 31.9 - - + -
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Residues in contact with ASP 186 (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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184A VAL* 4.1 2.2 + - + +
185A ILE* 1.3 71.9 - - - +
187A LEU* 1.3 64.0 + - - +
188A GLN* 3.0 20.8 + - - +
189A ALA* 3.0 26.0 + - + +
190A GLU* 3.0 26.1 + - - +
267A ARG* 4.4 1.2 - - - +
268A PHE* 3.6 29.1 - - + -
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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