Contacts of the strand formed by residues 228 - 234 (chain A) in PDB entry 3RKR
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A SER* 3.5 15.1 - - - -
218A LEU* 5.5 1.8 - - + +
219A LEU* 3.6 25.0 - - + +
222A GLN* 2.7 37.1 + - + +
226A SER* 4.3 4.5 - - - +
227A PHE* 1.3 78.5 - - - +
229A SER* 1.3 59.7 + - - +
230A GLU 3.9 3.8 - - - +
231A VAL* 3.7 21.1 - - + -
215D VAL* 4.1 29.2 - - + -
218D LEU* 4.4 18.2 - - + -
231D VAL* 3.7 11.7 - - + -
232D LEU 3.5 12.3 - - - +
233D VAL* 4.4 4.5 - - + +
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Residues in contact with SER 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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171A ALA* 5.7 0.4 - - - -
181A VAL 4.2 3.5 - - - +
182A SER* 3.3 6.9 - - - -
183A LEU* 3.0 25.1 + - - +
227A PHE* 3.3 9.8 + - - -
228A ILE* 1.3 74.1 - - - +
230A GLU* 1.3 62.4 + - - +
187D GLY* 3.7 14.7 + - - -
232D LEU* 2.8 18.1 + - - +
234D ARG* 3.4 46.0 - - - +
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Residues in contact with GLU 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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145A ALA* 5.0 6.6 - - - +
164A ASN* 5.7 2.3 + - - -
168A THR* 5.7 0.2 + - - -
182A SER* 5.3 0.2 - - - -
183A LEU* 3.3 34.4 - - + +
185A ALA* 4.3 8.2 - - + +
228A ILE* 3.6 2.1 - - - +
229A SER* 1.3 84.2 + - - +
231A VAL* 1.3 67.8 + - - +
232A LEU* 3.3 31.2 - - + +
230D GLU 4.1 0.2 - - - +
231D VAL* 3.5 2.9 - - - -
232D LEU* 2.9 60.8 + - + +
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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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183A LEU 2.9 8.3 + - - +
184A VAL* 3.5 4.7 - - + +
185A ALA 3.1 24.4 + - - +
215A VAL* 3.7 34.1 - - + -
219A LEU* 4.2 12.6 - - + -
228A ILE* 3.7 20.9 - - + -
230A GLU* 1.3 78.8 - - - +
232A LEU* 1.3 68.2 + - - +
233A VAL* 4.3 4.3 - - + -
228D ILE* 3.7 35.4 - - + -
230D GLU 3.6 3.4 - - - +
231D VAL* 4.6 7.4 - - + -
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Residues in contact with LEU 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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145A ALA* 4.5 9.6 - - + -
147A LYS* 5.8 1.1 - - - +
185A ALA* 3.2 20.2 - - + +
186A PRO 4.1 4.9 - - - +
187A GLY* 3.7 17.3 - - - +
230A GLU* 3.3 30.1 - - + +
231A VAL* 1.3 79.3 - - - +
233A VAL* 1.3 61.5 + - - +
228D ILE* 3.6 5.5 - - - +
229D SER* 2.9 35.7 + - - +
230D GLU* 2.9 44.8 + - + +
232D LEU* 6.2 2.2 - - + -
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Residues in contact with VAL 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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184A VAL* 4.3 17.0 - - + -
185A ALA 2.8 13.6 + - - +
186A PRO* 3.2 8.5 - - - +
187A GLY 2.8 23.6 + - - -
207A ILE* 3.8 30.5 - - + +
211A ASP* 4.9 9.4 - - + +
212A ILE* 5.1 6.1 - - + -
215A VAL* 4.1 25.6 - - + -
231A VAL* 4.3 5.6 - - + -
232A LEU* 1.3 79.2 - - - +
234A ARG* 1.3 70.4 + - - +
235A PRO* 4.6 0.3 - - - +
226D SER* 6.1 0.4 - - - -
227D PHE 3.6 15.9 - - - +
228D ILE* 4.8 2.7 - - + -
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Residues in contact with ARG 234 (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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187A GLY 3.7 25.3 + - - +
188A SER* 3.9 8.6 - - - +
207A ILE* 4.1 3.3 - - - +
211A ASP* 5.3 0.2 - - - +
233A VAL* 1.3 83.6 - - - +
235A PRO* 1.4 74.0 - - + +
236A THR 3.3 2.4 + - - -
168D THR* 3.6 30.5 + - - +
171D ALA* 3.9 9.2 - - - +
172D GLU* 2.7 46.8 + - - +
175D ARG* 3.9 1.4 - - - +
227D PHE* 2.9 50.0 + - + +
229D SER* 3.4 33.3 - - - +
240D SO4 3.2 19.3 + - - +
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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