Contacts of the strand formed by residues 226 - 232 (chain A) in PDB entry 2R3A
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 LEU 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A VAL* 3.6 34.5 - - + -
167A MET* 4.6 9.9 - - + -
218A VAL* 4.5 6.7 - - + -
224A PRO* 3.8 12.8 - - - +
225A ASN* 1.3 93.9 - - - +
227A GLN* 1.3 62.1 + - - +
245A LEU* 4.1 31.6 - - + +
246A PHE 3.2 12.8 - - - +
247A SER* 4.0 2.5 - - - +
248A THR* 3.8 3.1 - - - +
251A ILE* 4.1 9.0 - - + -
257A LEU* 3.9 23.1 - - + -
258A THR 2.9 18.3 + - - +
259A PHE* 3.6 23.7 - - + +
260A ASP 4.5 0.5 + - - -
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Residues in contact with GLN 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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107A ILE* 5.9 0.5 - - - +
111A PRO* 3.5 32.8 - - + +
163A MET* 5.2 7.8 - - - +
226A LEU* 1.3 76.3 - - - +
228A VAL* 1.3 66.4 + - - +
229A PHE* 3.7 26.7 - - + -
244A ALA 3.4 0.5 - - - +
245A LEU* 3.3 6.7 - - - -
246A PHE* 2.9 30.1 + - - +
247A SER 4.8 2.4 - - - +
248A THR* 3.5 27.1 - - + +
259A PHE* 5.4 0.7 - - - -
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Residues in contact with VAL 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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111A PRO* 5.1 5.5 - - - +
112A GLY 5.2 2.1 + - - -
195A PHE* 3.7 25.1 - - + -
227A GLN* 1.3 77.7 - - - +
229A PHE* 1.3 80.8 + - - +
230A ASN* 4.8 9.9 - - - +
243A ILE* 3.9 17.0 - - + -
244A ALA 3.4 4.3 - - - -
245A LEU* 3.8 18.8 - - + -
259A PHE* 4.9 8.7 - - + -
263A MET 4.0 19.4 + - - +
264A LYS* 3.8 15.3 - - - +
265A GLY* 5.9 0.2 - - - -
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Residues in contact with PHE 229 (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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107A ILE* 3.7 35.0 - - + -
109A ILE* 3.7 20.2 - - + -
110A PRO 3.6 21.5 - - - -
111A PRO* 3.7 17.9 - - + -
112A GLY 4.8 1.6 - - - +
113A THR 3.6 18.4 - - - -
115A ILE* 3.5 19.7 - - + -
227A GLN* 3.7 31.0 - - + -
228A VAL* 1.3 83.9 - - - +
230A ASN* 1.3 64.0 + - - +
231A VAL* 3.8 0.7 - - - +
243A ILE* 3.6 4.2 - - - -
244A ALA 2.8 34.2 + - - +
246A PHE* 3.9 22.2 - + + -
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Residues in contact with ASN 230 (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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112A GLY* 5.6 7.1 + - - -
113A THR 4.7 3.2 + - - -
114A PRO* 3.7 6.2 - - + +
115A ILE* 2.8 34.7 + - - +
197A LEU* 5.6 0.5 - - - +
199A TYR* 3.5 42.4 + - + +
228A VAL* 5.0 8.3 - - - +
229A PHE* 1.3 78.3 - - - +
231A VAL* 1.3 55.2 + - - +
232A PHE* 4.4 8.5 - - + -
241A PRO* 3.2 31.1 - - + +
242A ARG 3.4 4.0 - - - +
243A ILE* 5.1 5.9 - - - +
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Residues in contact with VAL 231 (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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115A ILE* 3.4 19.7 - - + +
117A GLU* 4.2 8.3 - - + -
133A VAL* 4.1 18.2 - - + -
229A PHE 3.8 4.0 - - - +
230A ASN* 1.3 79.3 - - - +
232A PHE* 1.3 68.7 + - - +
233A ILE* 3.8 29.4 - - + -
235A ASN* 3.1 7.3 + - - -
241A PRO* 4.2 0.2 - - - +
242A ARG* 2.8 50.1 + - + +
243A ILE 4.6 0.2 - - - -
244A ALA* 3.6 31.9 - - + +
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Residues in contact with PHE 232 (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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114A PRO* 3.7 21.5 - - + -
115A ILE 2.8 12.3 + - - -
116A TYR* 3.4 43.2 - + + +
117A GLU 3.0 27.0 + - - +
199A TYR* 3.8 22.4 - + - -
230A ASN* 4.4 7.9 - - + -
231A VAL* 1.3 74.2 - - - +
233A ILE* 1.3 63.4 + - - +
235A ASN* 3.1 32.3 - - - +
236A LEU* 4.4 5.2 - - + -
237A ASP 3.7 4.7 - - - -
238A THR* 3.6 26.9 - - + -
241A PRO* 3.6 30.5 - - + -
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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