Contacts of the strand formed by residues 225 - 233 (chain A) in PDB entry 1EGD
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 ILE 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A CYS* 3.9 17.7 - - - -
163A GLN* 3.3 4.2 - - - +
164A LYS* 2.8 36.5 + - + +
167A ILE* 4.0 15.7 - - + -
170A GLY* 4.2 4.5 - - - -
176A TYR* 3.5 37.5 - - + +
206A ILE* 3.6 30.5 - - + -
207A GLN 3.4 10.1 - - - +
208A ILE* 4.4 9.2 - - + -
223A ARG 4.9 1.1 - - - +
224A GLY* 1.3 82.2 - - - +
226A VAL* 1.3 69.1 + - - +
227A PHE* 4.0 18.3 + - + -
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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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162A GLY 3.8 11.0 - - - +
163A GLN* 4.3 18.4 - - + +
205A GLY 3.0 4.7 - - - +
206A ILE* 3.4 2.4 - - - -
207A GLN* 2.8 74.0 + - + +
225A ILE* 1.3 76.8 - - - +
227A PHE* 1.2 62.4 + - - +
228A GLU* 3.9 14.8 - - - +
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Residues in contact with PHE 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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134A CYS* 4.3 14.6 - - - -
149A THR* 5.1 1.6 - - + -
160A ILE* 4.1 18.8 - - + -
161A ASN* 3.2 8.7 - - - +
162A GLY 2.9 42.5 + - - +
164A LYS* 3.7 27.6 - - + -
176A TYR* 4.7 6.1 - + - -
178A LEU* 4.1 21.5 - - + -
199A VAL* 4.5 15.3 - - + -
206A ILE* 4.1 24.0 - - + -
225A ILE* 4.0 26.7 - - + -
226A VAL* 1.2 73.4 - - - +
228A GLU* 1.3 61.2 + - - +
229A ASP 3.7 0.4 - - - -
230A VAL* 3.3 29.4 - - + -
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Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A ASN* 3.8 6.1 - - - +
205A GLY* 2.7 24.4 + - - +
207A GLN* 3.0 27.3 + - - +
226A VAL* 3.9 13.1 - - - +
227A PHE* 1.3 71.9 - - - +
229A ASP* 1.3 72.8 + - + +
230A VAL* 3.3 1.1 - - - +
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Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.2 22.2 - - + +
160A ILE 3.3 8.3 + - - -
161A ASN* 3.0 32.1 + - - +
204A PRO 4.5 2.8 - - - +
228A GLU* 1.3 79.4 - - - +
230A VAL* 1.3 66.8 + - - +
231A LYS* 3.2 17.2 + - - +
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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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159A ILE* 3.5 1.3 - - - -
160A ILE* 2.8 39.6 + - + +
199A VAL* 5.6 4.3 - - + -
203A THR* 3.3 27.1 - - + -
204A PRO 3.6 7.6 - - - +
205A GLY 3.6 12.6 - - - -
206A ILE* 3.5 20.0 - - + -
227A PHE* 3.3 48.9 - - + -
228A GLU 3.4 6.1 - - - +
229A ASP* 1.3 76.0 - - - +
231A LYS* 1.3 62.9 + - - +
232A VAL* 3.8 6.9 + - + +
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Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LYS* 6.3 1.3 - - - -
157A GLU* 3.3 33.0 - - - +
158A TYR 3.8 0.9 - - - -
159A ILE* 4.4 18.5 - - + +
199A VAL* 6.1 0.2 - - - +
203A THR* 3.6 23.5 + - + +
204A PRO* 4.5 7.3 + - + +
229A ASP 3.8 12.4 + - - +
230A VAL* 1.3 72.7 - - - +
232A VAL* 1.3 62.2 + - - +
233A PRO* 4.0 6.8 - - - +
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Residues in contact with VAL 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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157A GLU* 3.4 4.0 + - - -
158A TYR* 2.8 43.3 + - - +
160A ILE* 3.4 32.8 - - + -
197A PHE* 4.1 19.5 - - + -
198A ILE 3.9 11.4 - - - +
199A VAL* 3.8 22.4 - - + -
230A VAL* 3.9 7.4 - - + +
231A LYS* 1.3 79.3 - - - +
233A PRO* 1.3 71.0 - - + +
236A ASN* 3.8 22.9 - - + +
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Residues in contact with PRO 233 (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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119A LYS* 6.3 0.9 - - - +
156A ASP 4.2 1.3 - - - +
157A GLU* 4.2 9.0 - - + -
158A TYR* 5.1 0.2 - - - -
231A LYS* 4.0 6.1 - - + +
232A VAL* 1.3 93.2 - - + +
234A LYS* 1.3 66.4 + - - +
235A GLU* 3.9 21.8 - - - +
236A ASN* 3.0 41.2 + - - +
237A VAL* 4.0 3.3 + - - +
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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