Contacts of the strand formed by residues 181 - 187 (chain d) in PDB entry 4B2Q
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 PHE 181 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89d ARG* 3.9 21.3 - - + -
92d LEU* 3.6 34.5 - - + -
178d HIS* 4.5 0.9 - - - -
180d GLY* 1.3 79.7 - - - -
182d SER* 1.3 65.1 + - - +
213d SER 4.5 6.1 - - - -
214d LYS* 3.4 17.7 - - + +
243d PHE* 4.2 30.7 - + + -
247d GLU* 4.0 20.9 - - + -
249d GLN* 3.6 25.6 - - + -
250d ASP 3.6 8.5 + - - +
251d VAL* 3.2 11.3 - - + -
252d LEU* 3.0 22.0 + - - +
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Residues in contact with SER 182 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92d LEU* 5.0 1.2 - - - +
175d ALA* 4.5 13.6 + - - +
178d HIS* 5.4 0.5 + - - +
180d GLY 5.3 0.3 + - - -
181d PHE* 1.3 75.3 - - - +
183d VAL* 1.3 69.2 + - - +
214d LYS 2.9 8.3 + - - -
215d VAL* 3.0 22.0 - - - -
216d ALA 2.9 24.3 + - - -
251d VAL* 4.7 0.2 - - - -
252d LEU* 3.2 38.9 - - - +
254d PHE* 4.7 9.2 - - - -
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Residues in contact with VAL 183 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182d SER* 1.3 80.8 - - - +
184d PHE* 1.3 64.2 + - - +
185d THR* 4.0 10.1 - - - +
215d VAL* 4.7 0.4 - - - -
216d ALA* 3.6 14.6 - - + +
218d VAL* 5.0 4.0 - - + -
236d GLY* 3.7 23.1 - - - +
239d ILE* 4.5 15.3 - - + -
240d ALA* 4.1 25.1 - - + +
243d PHE* 4.7 7.2 - - + -
251d VAL* 4.7 6.1 - - + -
252d LEU 2.7 9.8 + - - +
253d LEU* 3.5 18.3 - - + +
254d PHE* 2.8 29.0 + - - -
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Residues in contact with PHE 184 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167d ILE* 4.9 10.1 - - + -
168d GLN* 6.0 4.0 - - + -
171d ILE* 3.7 28.9 - - + -
182d SER 4.3 0.2 - - - -
183d VAL* 1.3 73.7 - - - +
185d THR* 1.3 85.1 + - - +
186d GLY* 3.9 19.3 - - - -
197d LEU* 3.5 35.0 - - + -
201d MET* 6.0 2.2 - - + -
215d VAL* 4.3 4.6 - - + +
216d ALA 3.1 7.1 + - - +
217d LEU* 3.6 19.0 - - + +
218d VAL* 2.9 27.0 + - - +
219d PHE* 4.2 11.4 - + - -
254d PHE* 3.5 19.3 - + + -
256d ASP* 4.5 21.5 - - + -
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Residues in contact with THR 185 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183d VAL* 4.0 6.6 - - - +
184d PHE* 1.3 79.5 + - - +
186d GLY* 1.3 60.8 + - - +
187d VAL* 3.5 23.8 + - + +
218d VAL* 3.1 10.7 - - + +
232d VAL* 3.7 23.6 - - + +
233d ALA* 4.2 6.9 + - - +
236d GLY* 3.7 22.2 - - - -
253d LEU* 4.5 3.3 - - - +
254d PHE 2.7 13.5 + - - -
255d ILE* 3.6 11.5 - - + -
256d ASP 3.1 25.1 + - - +
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Residues in contact with GLY 186 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184d PHE* 3.9 10.0 - - - -
185d THR* 1.3 69.0 - - - +
187d VAL* 1.3 62.0 + - - +
189d GLU* 5.5 0.7 - - - -
218d VAL 2.9 11.9 + - - +
219d PHE* 4.0 4.9 - - - -
220d GLY 2.8 30.7 + - - -
221d GLN* 3.5 23.6 + - - -
232d VAL* 4.2 0.3 - - - +
256d ASP 3.2 9.6 - - - -
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Residues in contact with VAL 187 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185d THR* 3.5 26.5 - - + +
186d GLY* 1.3 70.1 - - - -
188d GLY* 1.3 65.8 + - - +
189d GLU 3.5 0.2 - - - -
220d GLY 3.9 2.2 - - - -
229d ARG* 3.5 16.6 - - - +
232d VAL* 3.4 31.4 - - + -
233d ALA* 4.1 14.1 - - + +
255d ILE* 4.6 6.1 - - + -
256d ASP 2.9 8.7 + - - -
257d ASN 3.0 35.5 + - - +
260d ARG* 3.1 21.6 - - + +
261d PHE* 4.3 7.2 - - + +
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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