Contacts of the helix formed by residues 171 - 177 (chain A) in PDB entry 1R00
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 TYR 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A CYS* 3.3 39.7 + - + +
167A GLU 5.3 1.8 - - - -
168A ASP 5.3 1.1 + - - -
169A LEU 3.2 0.4 - - - -
170A ALA* 1.3 83.4 - - + +
172A GLU* 1.3 62.1 + - - +
173A ALA 3.4 2.9 - - - -
174A PRO* 3.5 7.9 - - + +
175A ALA* 3.1 25.6 + - - +
193A ASN* 5.7 3.2 + - - -
195A GLY* 3.5 28.7 - - - +
196A MET* 3.4 39.9 - - + +
199A ALA* 4.1 7.4 - - + -
224A ARG* 5.3 4.3 - - - -
255A SER* 3.9 5.8 - - - -
256A PHE* 4.4 12.3 - + - -
286A LEU* 4.6 4.0 - - + -
421A ACT 3.7 5.4 - - + +
635A SAH 2.8 40.0 + - - -
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Residues in contact with GLU 172 (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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168A ASP 5.1 2.6 - - - +
169A LEU* 3.3 40.9 + - + +
170A ALA 3.4 0.2 - - - -
171A TYR* 1.3 78.2 - - - +
173A ALA* 1.3 57.4 + - - +
175A ALA* 3.6 5.2 - - - +
176A ASP* 3.0 38.5 + - - +
199A ALA* 4.2 7.8 - - - +
202A LEU* 5.7 3.1 - - - +
203A ARG* 3.2 33.0 + - - +
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Residues in contact with ALA 173 (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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169A LEU 4.7 1.4 + - - -
170A ALA 4.8 0.4 + - - +
172A GLU* 1.3 76.9 - - - +
174A PRO* 1.3 73.3 - - + +
176A ASP* 3.1 9.8 + - - +
177A ALA* 3.0 18.4 + - - +
340A GLY 4.2 4.7 - - - +
341A SER* 3.8 23.1 - - - -
348A PHE* 3.6 23.5 - - + -
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Residues in contact with PRO 174 (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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170A ALA 4.0 9.4 - - - +
171A TYR* 3.5 24.5 - - + +
173A ALA* 1.3 95.9 - - + +
175A ALA* 1.3 60.2 + - - +
177A ALA* 3.2 10.2 + - - +
178A TYR* 3.8 3.6 + - - +
196A MET* 3.8 7.4 - - + +
256A PHE* 6.1 1.1 - - + -
286A LEU* 3.7 35.7 - - + -
341A SER* 5.6 0.2 - - - -
344A LEU* 5.6 3.6 - - + -
348A PHE* 3.4 34.1 - - + -
350A ILE* 3.5 17.9 - - + +
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Residues in contact with ALA 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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171A TYR 3.1 20.3 + - - +
172A GLU 3.6 4.5 - - - +
174A PRO* 1.3 77.6 - - - +
176A ASP* 1.3 60.6 + - - +
178A TYR 3.6 2.6 - - - +
180A TRP* 2.9 29.5 + - - +
196A MET* 3.5 16.7 - - + +
199A ALA* 4.0 15.9 - - + +
200A ILE 4.7 0.2 - - - +
203A ARG* 3.6 28.1 - - - +
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Residues in contact with ASP 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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172A GLU* 3.0 28.4 + - - +
173A ALA* 3.1 9.2 + - - +
175A ALA* 1.3 74.5 - - - +
177A ALA* 1.3 56.0 + - - +
178A TYR 3.2 11.8 + - - +
203A ARG* 3.0 30.6 + - - +
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Residues in contact with ALA 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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173A ALA 3.0 14.6 + - - +
174A PRO 3.2 7.3 + - - +
176A ASP* 1.3 76.2 - - - +
178A TYR* 1.3 56.7 + - - +
337A ARG* 2.8 41.3 + - + -
339A SER* 5.6 4.5 - - - -
348A PHE* 4.2 18.8 - - + -
350A ILE* 4.5 2.9 - - + -
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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