Contacts of the strand formed by residues 223 - 231 (chain A) in PDB entry 3J2I
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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12A ILE* 3.8 30.3 - - + -
21A TYR* 3.9 21.8 - - + +
189A GLN* 3.2 11.5 - - - +
190A LEU* 2.8 49.3 + - + +
221A HIS 4.5 2.5 - - - +
222A GLU* 1.3 79.1 - - - +
224A TYR* 1.3 65.9 - - - +
322A THR* 3.8 21.3 - - + -
323A VAL 3.4 11.9 - - - +
324A LEU* 4.0 11.9 - - + -
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Residues in contact with TYR 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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157A VAL* 4.1 15.3 - - + -
187A SER* 4.8 5.2 - - - -
188A HIS 3.6 5.4 - - - +
189A GLN* 3.5 35.2 - - + -
190A LEU* 4.4 1.6 - - - +
199A LYS* 3.2 33.9 - - + +
200A THR* 5.1 2.0 - - - -
201A ILE* 5.0 5.6 - - + -
218A PHE* 3.5 30.5 - + - -
222A GLU* 2.6 41.5 + - + -
223A VAL* 1.3 75.5 - - - +
225A ALA* 1.3 59.9 + - - +
226A VAL* 3.6 14.9 + - + +
322A THR* 3.3 6.8 - - - +
323A VAL* 2.9 43.8 + - + +
325A LEU* 4.0 11.2 - - + -
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Residues in contact with ALA 225 (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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120A ASN* 3.8 29.8 - - + +
187A SER* 3.4 21.2 - - - -
188A HIS* 3.1 13.9 + - + +
190A LEU* 4.0 14.8 - - + +
224A TYR* 1.3 69.5 - - - +
226A VAL* 1.3 63.5 + - - +
227A ASP* 3.5 3.8 + - - +
320A LYS* 4.7 6.5 - - + -
321A PHE 3.4 7.4 - - - +
322A THR* 4.0 11.9 - - - +
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Residues in contact with VAL 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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153A ALA* 3.7 27.4 - - + -
157A VAL* 4.2 20.6 - - + -
170A TRP* 3.8 15.9 - - + -
187A SER* 3.7 5.6 - - - +
201A ILE* 4.6 5.4 - - + -
224A TYR* 3.6 17.0 - - + -
225A ALA* 1.3 71.6 - - - +
227A ASP* 1.3 60.5 + - - +
228A VAL* 4.2 4.3 - - + -
319A PHE 4.0 0.7 - - - +
320A LYS* 3.1 5.5 - - - +
321A PHE* 2.8 67.3 + - + +
323A VAL* 4.2 5.6 - - + -
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Residues in contact with ASP 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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170A TRP* 4.1 5.3 - - - -
185A MET* 5.6 1.6 - - - +
186A LEU 4.3 16.1 - - - +
187A SER* 2.8 21.7 + - - +
203A GLN* 3.6 12.8 - - - +
225A ALA 4.2 4.7 - - - +
226A VAL* 1.3 74.4 - - - +
228A VAL* 1.3 62.4 + - - +
229A LEU* 3.7 19.1 + - - +
318A GLN* 2.9 27.0 + - - +
319A PHE 3.9 1.1 - - - -
320A LYS* 3.3 32.0 + - + +
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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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146A ALA* 3.5 26.0 - - + +
149A CYS* 3.6 12.1 - - + -
150A ALA* 3.8 24.9 - - - +
170A TRP* 3.7 30.5 - - + +
203A GLN* 3.4 5.6 - - - +
226A VAL* 4.6 4.7 - - + -
227A ASP* 1.3 72.5 + - - +
229A LEU* 1.3 62.6 + - - +
230A VAL* 3.7 17.7 - - + -
318A GLN* 3.0 28.2 - - - +
319A PHE* 2.9 19.6 + - - +
321A PHE* 5.7 0.2 - - + -
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Residues in contact with LEU 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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86A VAL* 3.6 34.3 - - + +
87A CYS* 5.0 3.6 - - + -
181A PRO* 3.5 1.2 - - - +
182A ILE* 3.0 35.9 + - + -
185A MET* 3.5 28.7 - - + -
203A GLN* 2.8 20.3 + - - +
227A ASP* 3.7 28.7 - - - +
228A VAL* 1.3 75.1 - - - +
230A VAL* 1.3 62.2 + - - +
316A VAL* 4.3 6.3 - - + -
317A ALA 3.4 4.3 - - - -
318A GLN* 3.8 27.1 - - + +
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Residues in contact with VAL 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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142A VAL* 3.2 10.4 - - + +
145A ALA* 4.2 7.0 - - + -
146A ALA* 3.9 18.2 - - + -
149A CYS* 4.3 13.2 - - - -
174A ALA* 4.1 8.3 - - + -
179A CYS* 3.6 28.0 - - + -
180A THR 3.7 11.9 - - - +
181A PRO* 4.3 11.2 - - + -
182A ILE* 4.4 0.6 - - - +
228A VAL* 3.7 23.3 - - + -
229A LEU* 1.3 78.6 - - - +
231A SER* 1.3 61.6 + - - +
316A VAL* 3.3 5.5 - - - +
317A ALA 2.9 33.2 + - - -
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Residues in contact with SER 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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142A VAL* 3.7 4.5 - - - -
179A CYS* 3.2 6.2 - - - +
180A THR 2.8 41.1 + - - -
182A ILE* 4.3 4.5 - - - +
229A LEU 4.4 0.2 + - - -
230A VAL* 1.3 74.0 - - - +
232A SER* 1.3 60.0 + - - +
233A GLY 2.9 16.8 + - - +
235A GLY* 4.2 5.2 - - - -
310A GLU* 2.6 43.7 + - - +
314A GLU* 4.6 1.2 - - - +
315A PHE 3.5 7.4 + - - -
316A VAL* 4.2 3.4 - - - +
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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