Contacts of the helix formed by residues 201 - 205 (chain A) in PDB entry 1XR2
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 PRO 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A PHE* 4.5 5.4 - - + -
106A PHE* 3.5 32.3 - - + -
148A ILE* 5.9 1.1 - - + -
152A THR* 3.4 12.6 - - + +
199A ASN* 3.2 17.0 - - + +
200A GLU* 1.3 84.2 - - - +
202A ALA* 1.3 56.1 + - - +
203A PHE 2.9 6.1 - - - -
204A VAL* 2.8 36.6 + - - +
230A PHE 4.0 0.2 - - - -
231A THR* 4.5 0.2 - - - -
232A TYR* 3.9 50.0 - - + +
233A TYR* 4.4 2.2 - - + -
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Residues in contact with ALA 202 (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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106A PHE* 3.8 12.5 - - + -
151A PHE* 3.9 21.1 - - + -
152A THR* 3.1 29.2 + - + +
155A TYR* 4.0 20.2 - - + -
201A PRO* 1.3 79.1 - - - +
203A PHE* 1.3 61.7 + - - +
204A VAL 2.9 2.0 + - - -
205A CYS* 3.1 21.4 + - - +
207A LEU* 3.8 10.6 - - - +
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Residues in contact with PHE 203 (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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151A PHE* 3.8 18.8 - + - -
200A GLU* 3.1 48.5 + - + +
201A PRO 2.9 0.6 + - - -
202A ALA* 1.3 78.6 - - - +
204A VAL* 1.3 58.7 + - - +
205A CYS 3.3 0.4 - - - -
207A LEU* 4.1 5.4 - - - -
212A TRP* 3.8 19.7 - + + -
215A ILE* 3.3 45.3 - - + -
219A TYR* 4.1 7.2 - + - -
229A VAL* 4.3 9.2 - - + -
231A THR* 3.9 20.2 - - + -
236A VAL* 3.8 4.6 - - + -
237A SER* 3.0 33.1 + - - -
242A CYS* 4.3 5.6 - - - -
245A LEU* 4.1 19.5 - - + -
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Residues in contact with VAL 204 (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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106A PHE* 5.1 1.8 - - + -
201A PRO 2.8 23.6 + - - +
203A PHE* 1.3 79.7 - - - +
205A CYS* 1.3 61.3 + - - +
231A THR* 4.3 10.1 - - - -
232A TYR 3.8 28.9 - - - +
234A ASP* 3.0 36.5 - - + +
235A SER 3.4 18.8 - - - +
236A VAL* 4.3 1.1 - - - +
587A ILE* 4.2 21.4 - - + +
588A LYS* 2.6 32.2 + - - +
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Residues in contact with CYS 205 (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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106A PHE* 4.1 5.8 - - - -
155A TYR* 3.4 37.0 - - + +
202A ALA* 3.1 25.5 + - - +
204A VAL* 1.3 81.5 - - - +
206A ASP* 1.3 55.3 + - - +
207A LEU* 2.7 24.0 + - + +
237A SER* 3.2 13.4 - - - -
587A ILE* 3.8 16.2 - - - +
588A LYS* 4.4 1.1 - - - -
1205A MRY 3.4 26.7 - - - +
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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