Contacts of the helix formed by residues 175 - 180 (chain A) in PDB entry 5OO2
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 HIS 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE* 4.2 5.8 - - + -
173A LEU* 3.5 7.1 - - - +
174A TYR* 1.3 78.1 - - - +
176A GLY* 1.3 68.6 + - - +
177A TRP* 3.0 56.6 + + + +
178A GLU* 3.0 34.3 + - + +
179A SER 4.1 0.5 + - - -
191A TYR* 3.7 13.5 - - - -
225A TYR* 2.8 36.5 + + + -
228A LEU* 3.5 26.2 - - + +
229A LEU* 3.8 13.9 - - + +
232A MET* 4.1 13.0 - - + -
248A PHE* 3.5 8.8 - - - -
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Residues in contact with GLY 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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173A LEU* 5.4 0.7 - - - -
175A HIS* 1.3 71.2 + - - +
177A TRP* 1.3 62.7 + - - +
178A GLU 3.1 0.2 - - - -
179A SER* 2.8 26.5 + - - -
180A GLY 4.0 0.7 + - - -
182A ASP* 4.0 10.6 - - - -
187A TRP* 4.2 13.9 + - - -
191A TYR* 3.0 25.5 + - - -
248A PHE* 3.6 18.6 - - - -
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Residues in contact with TRP 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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78A HIS* 4.5 8.5 - - - +
88A TYR* 4.9 1.3 - - - -
90A PRO* 3.9 25.1 - - + -
95A TRP* 4.0 13.7 - + - -
113A ILE* 3.6 24.5 - - + -
114A THR 4.6 0.4 - - - -
115A GLN* 3.9 12.1 + - - +
175A HIS* 3.0 34.8 + + - +
176A GLY* 1.3 76.6 - - - +
178A GLU* 1.3 61.8 + - - +
180A GLY* 3.1 15.2 + - - -
182A ASP* 3.4 42.1 + - + +
191A TYR* 4.2 0.2 + - - -
222A TYR* 4.6 14.6 + + - -
225A TYR* 3.6 40.1 - + + -
226A LEU* 4.7 8.5 - - + -
229A LEU* 3.9 15.7 - - + -
507A 9YW 4.0 22.8 + - - +
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Residues in contact with GLU 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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113A ILE* 3.3 23.9 - - + +
114A THR* 2.9 44.8 + - + +
115A GLN* 3.5 1.3 - - - -
116A PRO* 3.3 19.8 - - - +
163A ARG* 3.0 32.6 + - - -
173A LEU* 3.3 15.2 - - + -
174A TYR* 2.8 31.2 + - - -
175A HIS* 3.0 16.5 + - + +
177A TRP* 1.3 76.7 - - - +
179A SER* 1.3 59.9 + - - +
180A GLY 3.1 0.4 - - - -
255A PHE* 3.3 9.9 - - - -
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Residues in contact with SER 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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42A TRP* 4.5 3.8 - - - -
116A PRO* 3.8 13.6 - - - +
173A LEU* 3.6 8.0 - - - +
176A GLY 2.8 18.6 + - - -
178A GLU* 1.3 78.9 - - - +
180A GLY* 1.3 55.9 + - - +
181A MET* 2.9 25.8 + - - +
186A ARG* 4.5 4.2 + - - -
187A TRP* 3.1 29.5 + - - -
252A ASP* 3.0 27.6 - - - +
254A PHE* 5.3 2.6 - - - -
255A PHE* 4.5 1.2 - - - +
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Residues in contact with GLY 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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42A TRP* 3.7 23.1 - - - -
115A GLN* 4.3 4.9 - - - -
116A PRO* 4.3 1.5 - - - +
177A TRP 3.1 13.6 + - - -
178A GLU 3.1 1.8 + - - -
179A SER* 1.3 76.6 - - - +
181A MET* 1.3 59.4 + - - +
182A ASP* 3.7 5.6 - - - -
376A TRP* 3.2 7.4 + - - -
507A 9YW 2.7 33.3 + - - -
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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