Contacts of the strand formed by residues 222 - 228 (chain A) in PDB entry 2Q4E
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLY 5.2 0.6 + - - +
182A LEU 4.4 11.6 + - - +
183A GLY* 3.6 5.1 - - - -
184A ALA* 3.0 27.5 + - + +
185A LEU* 4.1 30.5 - - + +
215A VAL 3.4 5.2 - - - +
216A LEU* 3.3 23.3 - - + -
220A GLY 4.8 1.6 - - - +
221A VAL* 1.3 79.9 - - - +
223A LEU* 1.3 66.1 + - - +
224A SER* 3.6 16.6 - - - +
225A CYS* 3.8 26.2 - - + -
243A PHE* 4.1 0.5 - - - -
347A LYS* 4.9 17.5 - - + +
350A VAL* 4.7 15.3 - - + -
351A ASP* 6.0 1.3 - - - +
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Residues in contact with LEU 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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169A LEU* 4.3 17.5 - - + -
175A VAL* 4.5 12.8 - - + -
184A ALA* 3.7 6.7 - - - -
215A VAL* 2.4 39.1 + - + +
216A LEU 4.9 0.2 - - - +
217A ASN* 4.0 25.4 - - + +
221A VAL* 3.8 9.0 - - + +
222A ILE* 1.3 82.8 - - - +
224A SER* 1.3 57.9 + - - +
242A SER* 3.1 2.6 + - - -
243A PHE* 2.8 47.4 + - + -
244A LEU* 3.9 27.4 - - + +
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Residues in contact with SER 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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184A ALA* 4.6 0.4 - - - -
213A GLY 4.7 2.4 + - - -
214A ALA* 3.2 2.6 - - - +
215A VAL* 2.9 50.7 + - - +
222A ILE* 3.6 5.0 - - - +
223A LEU* 1.3 82.6 - - - +
225A CYS* 1.3 66.2 + - - +
240A TYR* 4.9 8.9 + - - -
241A CYS 3.3 8.3 - - - -
242A SER* 3.5 21.3 - - - -
244A LEU* 4.2 6.3 - - - +
234B GLY* 5.2 4.7 + - - -
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Residues in contact with CYS 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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185A LEU* 4.3 23.3 - - - -
211A PHE 5.5 2.7 - - - +
213A GLY 5.6 0.7 - - - -
214A ALA* 3.8 22.2 - - + +
222A ILE* 3.8 25.4 - - + -
224A SER* 1.3 76.5 - - - +
226A GLY* 1.3 60.2 + - - +
239A ILE* 5.5 1.1 - - - +
240A TYR* 3.9 10.9 - - - -
241A CYS* 3.1 34.3 + - - +
346A VAL* 4.6 6.7 - - - -
350A VAL* 4.5 13.0 - - + -
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Residues in contact with GLY 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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210A ALA* 3.3 7.8 - - - +
211A PHE* 3.2 44.0 + - - +
225A CYS* 1.3 77.4 - - - +
227A ALA* 1.3 66.5 + - - +
239A ILE* 3.5 14.8 - - - -
240A TYR* 4.0 4.4 - - - -
346A VAL* 4.4 4.6 - - - +
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Residues in contact with ALA 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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208A VAL* 4.5 0.7 - - + -
209A THR 3.0 19.7 - - - +
210A ALA* 3.5 6.5 - - - -
211A PHE* 3.0 17.9 - - - -
226A GLY* 1.3 77.3 - - - +
228A SER* 1.3 59.1 + - - +
229A LEU* 3.8 15.7 - - + +
238A THR* 3.0 24.3 - - - -
239A ILE* 3.1 11.6 + - + +
346A VAL* 3.9 22.0 - - + -
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Residues in contact with SER 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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208A VAL* 3.5 0.3 - - - -
209A THR* 2.6 46.7 + - - -
211A PHE* 3.4 6.3 - - - -
227A ALA* 1.3 71.8 - - - +
229A LEU* 1.3 63.1 + - - +
230A SER* 4.0 3.4 + - - -
236A THR* 5.8 3.4 - - - -
237A ALA 2.8 13.2 - - - -
238A THR* 4.0 9.9 - - - -
211B PHE* 4.0 19.0 - - - -
212B PRO* 3.5 26.7 - - - +
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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