Contacts of the strand formed by residues 220 - 226 (chain B) in PDB entry 2B4M
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 ALA 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B THR* 5.7 0.7 - - + -
102B ILE 3.4 11.4 - - - +
103B THR* 3.8 2.5 - - + -
107B PHE* 5.2 0.4 - - + -
118B LEU* 3.5 33.9 - - + -
171B ILE* 5.2 1.3 - - + -
172B ASN 3.2 2.6 + - - -
173B LEU* 3.3 21.0 - - + -
174B ALA* 2.7 33.4 + - - +
213B ILE* 3.7 5.4 - - - -
218B ALA 3.7 0.4 - - - -
219B ASP* 1.3 82.3 - - + +
221B SER* 1.3 58.3 + - - +
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Residues in contact with SER 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B HIS 4.0 0.2 - - - +
101B THR* 3.7 2.9 - - - +
102B ILE* 2.9 41.5 + - - +
173B LEU* 5.6 1.1 - - - -
174B ALA 3.0 21.6 + - - -
209B MET* 3.4 28.7 - - - +
213B ILE* 4.0 11.4 - - - -
220B ALA* 1.3 74.4 - - - +
222B LEU* 1.3 66.6 + - - +
223B SER* 3.2 16.0 + - - -
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 3.6 18.2 - - - +
100B HIS 3.8 9.9 - - - -
101B THR* 3.7 35.0 - - + +
118B LEU* 4.3 15.3 - - + +
121B PHE* 4.0 18.2 - - + -
173B LEU* 5.1 5.8 - - + -
174B ALA 4.1 3.2 + - - -
181B GLU* 3.6 10.2 - - - +
184B SER* 3.7 25.1 + - - +
185B THR* 3.7 36.4 + - + +
188B ILE* 3.8 21.3 - - + -
221B SER* 1.3 76.1 + - - +
223B SER* 1.3 59.6 + - - +
224B ALA 3.6 2.7 - - - -
247B SER* 5.3 1.8 - - - +
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Residues in contact with SER 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B TYR* 3.7 5.9 - - - +
176B VAL* 3.3 27.6 + - - +
181B GLU* 3.2 27.5 - - - +
185B THR* 4.5 0.5 + - - -
209B MET* 3.8 15.4 - - - +
221B SER* 3.2 16.2 + - - -
222B LEU* 1.3 78.6 + - - +
224B ALA* 1.3 61.0 + - - +
225B TRP* 3.3 9.5 + - - -
230B HIS* 3.2 20.8 - - - -
310B PBE 6.0 0.2 - - - +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU 3.7 0.3 - - - +
99B ILE* 3.4 4.3 - - - +
100B HIS* 2.7 48.8 + - + +
102B ILE* 3.9 28.7 - - + -
209B MET* 4.5 2.5 - - - +
210B TRP* 3.9 19.1 - - + -
221B SER* 4.6 1.2 + - - -
222B LEU 3.6 1.6 - - - -
223B SER* 1.3 74.8 - - - +
225B TRP* 1.3 60.7 + - - +
226B LEU* 3.9 5.8 - - + -
230B HIS* 3.9 7.0 - - - -
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Residues in contact with TRP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TRP* 4.1 11.9 - + + -
74B PRO* 4.0 26.9 - - + -
97B GLU* 3.6 6.3 - - + +
98B GLU 3.4 4.5 - - - -
99B ILE* 3.6 30.0 - - + +
180B SER* 4.0 10.8 - - - -
181B GLU* 3.1 25.9 + - - -
223B SER 3.3 14.5 + - - -
224B ALA* 1.3 74.8 - - - +
226B LEU* 1.3 63.0 + - - +
229B THR* 3.3 30.7 - - + +
230B HIS* 3.1 35.2 + - + +
251B VAL* 3.5 24.0 - - + -
252B LYS 5.2 0.2 - - - -
253B MET* 4.4 8.3 - - - -
310B PBE 3.6 49.4 - - + -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 3.1 5.4 - - - -
98B GLU* 2.7 38.8 + - - +
100B HIS* 3.8 34.5 - - + +
102B ILE* 5.0 1.6 - - + -
210B TRP* 4.2 11.9 - - + -
224B ALA* 3.9 21.7 - - + -
225B TRP* 1.3 83.5 - - - +
227B PRO* 1.3 67.5 - - + +
230B HIS* 3.7 24.9 - - + +
234B ALA* 3.9 20.0 - - + -
241B TYR* 4.4 8.5 - - - +
243B ASP* 4.1 8.1 - - - +
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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