Contacts of the strand formed by residues 223 - 228 (chain A) in PDB entry 1R5M
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 VAL 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A VAL* 3.6 26.0 - - - +
162A SER* 5.1 1.2 + - - -
176A GLY* 3.8 20.8 - - - -
177A GLU 3.1 10.4 + - - +
181A VAL* 3.3 42.0 - - - +
182A ALA* 3.9 8.3 - - + +
208A HIS* 4.8 5.2 - - + +
221A ASN 4.0 0.2 + - - -
222A GLN* 1.3 71.8 - - - +
224A THR* 1.3 60.5 + - - +
225A CYS 3.8 5.6 - - - +
226A LEU* 3.8 20.4 - - + -
237A THR* 4.7 2.2 - - - -
238A GLY 3.4 14.6 - - - +
239A VAL* 4.1 13.7 - - + -
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Residues in contact with THR 224 (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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161A VAL* 5.1 6.0 - - + +
162A SER* 4.8 8.8 + - - -
222A GLN* 3.4 17.9 + - + +
223A VAL* 1.3 74.6 - - - +
225A CYS* 1.3 62.1 + - - +
238A GLY 2.8 11.6 + - - -
239A VAL 3.9 2.3 - - - -
240A GLU* 3.7 24.7 - - + +
263A PRO* 4.4 9.0 - - + -
264A ILE* 2.8 38.0 + - - +
265A VAL* 5.2 2.4 - - - +
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Residues in contact with CYS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 5.0 1.6 - - - -
223A VAL* 3.6 3.0 - - - +
224A THR* 1.3 83.8 + - - +
226A LEU* 1.3 78.0 + - - +
227A ALA* 5.2 0.7 - - - -
236A VAL 4.5 0.4 - - - -
237A THR* 3.4 3.3 - - - -
238A GLY 2.9 28.9 + - - +
264A ILE* 3.8 24.5 - - + +
265A VAL 4.1 4.7 - - - -
266A SER* 4.1 10.5 - - - -
267A VAL* 3.7 39.9 - - - -
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Residues in contact with LEU 226 (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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162A SER* 3.3 28.7 + - - +
163A SER* 4.8 2.0 - - - +
164A THR* 3.7 23.8 - - + +
174A ALA* 4.0 13.5 - - + -
175A TYR 3.8 31.0 - - - +
176A GLY 3.8 13.0 - - - +
182A ALA* 4.0 15.3 - - + -
183A ARG 5.5 0.2 - - - +
206A LEU* 5.7 0.7 - - + -
223A VAL* 3.8 13.5 - - + -
225A CYS* 1.3 88.2 - - - +
227A ALA* 1.3 63.9 + - - +
235A ILE* 4.4 3.1 - - + -
236A VAL 3.3 7.0 - - - +
237A THR* 4.2 9.4 - - + -
1002A SO4 5.3 2.3 + - - -
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Residues in contact with ALA 227 (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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164A THR* 4.8 1.6 - - - -
225A CYS* 5.2 0.9 - - - -
226A LEU* 1.3 78.6 - - - +
228A TRP* 1.3 60.7 + - - +
235A ILE* 3.4 5.1 - - - +
236A VAL 2.9 34.3 + - - +
267A VAL* 3.6 44.0 - - + +
269A TRP* 3.0 16.6 + - + +
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Residues in contact with TRP 228 (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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164A THR* 2.9 41.9 + - + +
165A TRP 3.2 24.3 - - - -
166A ASN* 3.3 33.4 - - + -
167A PRO* 3.6 18.4 - - + -
172A ILE* 3.9 22.9 - - + -
174A ALA* 3.8 20.1 - - + +
184A LEU* 3.9 17.3 - - + -
227A ALA* 1.3 73.7 - - - +
229A SER* 1.3 64.8 + - - +
230A HIS* 3.9 2.1 + - - -
232A GLY 3.7 10.3 - - - -
234A SER 3.4 23.3 - - - -
235A ILE* 3.7 18.4 - - + +
249A LYS* 3.9 21.8 - - + -
269A TRP* 3.3 12.1 - - - +
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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