Contacts of the strand formed by residues 221 - 228 (chain A) in PDB entry 1EUT
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.8 20.9 - - + -
137A ASP* 3.2 30.3 - - + +
144A PHE* 3.5 27.6 - - + -
210A ILE 3.1 4.5 - - - +
211A GLN* 3.2 26.9 - - + +
219A GLY 4.0 2.0 - - - +
220A ARG* 1.3 74.8 - - - +
222A ILE* 1.3 59.3 + - - +
240A TYR* 3.0 29.1 - - - +
241A SER* 3.1 8.1 + - - +
244A HIS* 3.8 1.6 - - - -
245A GLY 3.6 21.3 - - - +
248A TRP* 3.7 21.8 - - + -
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Residues in contact with ILE 222 (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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135A LEU* 2.9 5.0 - - - +
209A GLY* 3.3 2.3 - - - -
210A ILE* 2.8 63.1 + - + +
212A LEU* 4.0 24.0 - - + -
220A ARG* 3.9 14.4 - - + +
221A LEU* 1.3 80.6 - - - +
223A GLN* 1.3 61.7 + - - +
224A GLN* 3.0 33.2 - - - +
238A SER* 3.6 17.3 - - - +
239A VAL 3.5 4.7 - - - +
240A TYR* 4.3 2.7 - - + -
248A TRP* 5.5 0.2 - - - -
263A THR* 4.1 3.2 + - - +
271A VAL* 4.6 5.4 - - + -
294A HIS* 4.0 23.8 - - + +
296A TYR* 5.2 0.2 - - - +
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Residues in contact with GLN 223 (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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133A SER* 2.7 37.6 + - - -
134A TYR 4.2 1.6 + - - -
135A LEU* 4.4 1.9 - - + +
146A PHE* 3.6 53.5 - - + -
204A ALA* 4.4 2.0 - - + -
205A ALA 3.2 15.6 + - - +
208A GLU 5.1 0.3 - - - -
209A GLY* 3.7 19.7 - - - +
222A ILE* 1.3 75.3 - - - +
224A GLN* 1.3 79.1 + - - +
225A TYR* 4.1 10.5 - - + -
239A VAL* 2.9 36.2 + - + +
248A TRP* 5.2 0.4 - - + -
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Residues in contact with GLN 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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204A ALA* 3.6 3.6 - - - -
205A ALA* 2.9 25.6 + - + -
209A GLY* 5.7 0.2 - - - -
222A ILE* 3.0 19.6 - - - +
223A GLN* 1.3 83.2 + - - +
225A TYR* 1.3 58.8 + - - +
237A VAL 3.8 3.0 - - - +
238A SER* 2.7 35.2 + - - -
261A ASN* 2.9 50.2 - - - +
262A LYS* 4.2 0.9 - - + -
263A THR* 2.7 46.2 + - + +
273A LEU* 4.2 4.9 - - - +
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Residues in contact with TYR 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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146A PHE* 3.5 20.1 - + - -
172A ALA* 4.0 14.7 - - + +
173A ASN 4.6 2.6 + - - -
189A ILE* 3.7 15.1 - - - +
193A ILE* 3.7 18.6 - - + +
202A ARG* 4.0 9.4 - - + -
203A PHE* 3.3 27.8 - - - -
204A ALA* 3.6 18.8 - - + +
205A ALA 4.4 1.8 - - - +
223A GLN* 3.6 16.4 - - + -
224A GLN* 1.3 78.4 - - - +
226A THR* 1.3 60.7 + - - +
227A ILE* 5.0 1.6 - - + -
236A ALA* 3.5 0.5 - - - -
237A VAL* 2.9 41.3 + - + +
239A VAL* 3.2 38.8 - - + -
261A ASN* 2.8 20.2 + - - -
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Residues in contact with THR 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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155A PHE* 3.7 17.5 - - + -
202A ARG* 3.1 24.3 - - - +
203A PHE* 3.2 24.7 + - + -
205A ALA* 5.4 0.5 - - - +
225A TYR* 1.3 74.2 + - - +
227A ILE* 1.3 68.7 + - - +
234A PHE* 4.4 6.7 - - + -
235A GLN 3.1 15.0 + - - +
258A MET 4.4 4.3 - - - +
259A ASP* 2.9 46.3 + - - +
260A GLU* 3.2 4.7 + - - -
261A ASN* 3.7 1.6 + - - -
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Residues in contact with ILE 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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155A PHE* 4.6 0.2 - - - -
199A TRP* 3.5 56.8 - - + +
201A SER 3.2 11.4 - - - +
202A ARG* 4.4 8.1 - - + -
226A THR* 1.3 79.7 - - - +
228A ILE* 1.3 65.6 + - - +
229A ASN 4.3 6.7 - - - +
234A PHE* 3.2 6.6 - - - -
235A GLN* 3.1 41.4 + - + +
237A VAL* 3.5 28.3 - - + -
253A ALA* 3.6 20.9 - - + -
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Residues in contact with ILE 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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155A PHE* 3.4 56.3 - - + +
156A ALA* 4.5 2.7 - - - -
199A TRP* 3.5 1.9 - - - -
200A ARG* 2.9 64.0 + - - +
201A SER* 3.1 19.9 + - - +
227A ILE* 1.3 76.2 - - - +
229A ASN* 1.3 68.2 + - - +
232A GLY* 4.0 22.2 - - - +
233A ALA 3.2 3.4 - - - +
234A PHE* 4.0 14.4 - - + -
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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