Contacts of the strand formed by residues 216 - 223 (chain B) in PDB entry 5CVE
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 HIS 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ASN* 3.4 2.4 - - - -
169B MET* 2.8 34.3 + - + +
171B GLN* 3.3 38.2 + - - +
206B ARG* 3.1 47.5 + - - +
210B LEU* 5.1 2.7 - - - -
212B ASP 5.5 3.7 + - - -
214B ILE 4.1 8.1 - - - -
215B TYR* 1.3 78.2 - - - +
217B VAL* 1.3 59.3 + - - +
218B TYR* 4.0 21.8 + - + -
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Residues in contact with VAL 217 (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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136B TRP* 3.9 21.3 - - + +
166B LYS* 4.0 27.1 - - + -
167B ASP 3.3 11.9 - - - +
168B ASN* 3.6 22.9 - - - +
206B ARG* 3.6 6.8 - - - +
207B GLN* 2.8 38.7 + - + -
210B LEU* 3.7 29.2 - - + +
214B ILE* 5.1 2.7 - - + -
215B TYR 3.8 3.8 - - - +
216B HIS* 1.3 77.3 - - - +
218B TYR* 1.3 68.1 + - - +
2E PRO* 5.5 0.2 - - + -
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Residues in contact with TYR 218 (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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165B ILE 3.6 1.4 - - - +
166B LYS* 3.2 4.7 - - - +
167B ASP 3.0 31.1 + - - +
169B MET* 3.6 21.8 - - + -
171B GLN* 5.9 0.7 - - - -
187B LEU* 4.0 27.3 - - + +
204B GLU* 3.9 26.7 - - + -
205B GLU 3.4 6.1 - - - -
206B ARG* 3.7 42.3 + - + +
207B GLN 5.4 0.2 - - - -
216B HIS* 4.0 24.2 + - + -
217B VAL* 1.3 80.1 - - - +
219B SER* 1.3 62.4 - - - +
220B PHE* 3.8 23.8 - - + -
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Residues in contact with SER 219 (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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45B SER* 5.8 0.7 - - - -
48B PHE* 3.8 33.8 - - - +
133B TRP* 5.6 0.6 - - - -
164B VAL* 4.8 2.5 - - - -
165B ILE 3.2 6.1 - - - -
166B LYS* 3.2 35.0 + - - +
203B ALA 3.9 0.2 - - - +
204B GLU* 3.3 6.1 - - - +
205B GLU* 2.9 38.6 + - - -
207B GLN* 5.8 0.9 - - - +
218B TYR* 1.3 72.9 - - - +
220B PHE* 1.3 63.1 + - - +
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Residues in contact with PHE 220 (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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48B PHE* 4.2 3.1 - - - -
163B ILE 3.6 1.6 - - - +
164B VAL* 3.2 5.5 - - - -
165B ILE* 2.7 54.7 + - + +
169B MET* 3.5 28.9 - - + -
187B LEU* 3.6 26.5 - - + -
190B VAL* 4.3 13.9 - - + -
191B ARG* 4.8 12.6 - - + -
194B ILE* 4.4 10.5 - - + -
201B LEU* 3.8 18.8 - - + -
203B ALA 3.4 4.7 - - - -
204B GLU* 3.6 34.8 - - + -
218B TYR* 3.8 15.7 - - + -
219B SER* 1.3 73.0 - - - +
221B ALA* 1.3 59.9 + - - +
222B LEU* 4.0 11.9 + - + +
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Residues in contact with ALA 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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48B PHE* 3.7 13.9 - - + -
52B PHE* 3.3 39.7 - - + -
162B ILE* 4.6 3.8 - - + -
163B ILE 3.5 4.3 - - - -
164B VAL* 4.3 7.0 - - + -
202B LEU* 2.8 35.6 + - + -
203B ALA 2.9 11.6 + - - +
220B PHE* 1.3 73.7 - - - +
222B LEU* 1.3 58.9 + - - +
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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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162B ILE* 3.3 5.2 - - - +
163B ILE* 2.7 47.1 + - + +
165B ILE* 3.9 24.2 - - + -
194B ILE* 3.7 46.9 - - + -
199B LEU* 4.1 20.6 - - + -
200B SER 3.3 13.5 - - - +
201B LEU* 3.8 19.7 - - + -
202B LEU* 3.9 4.7 - - - -
220B PHE* 4.0 6.7 - - + +
221B ALA* 1.3 85.4 - - - +
223B ARG* 1.3 65.4 + - - +
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Residues in contact with ARG 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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52B PHE* 5.0 5.1 - - - -
58B ASN* 4.0 24.7 + - - +
60B THR* 4.0 4.2 + - - -
154B LYS* 2.6 29.9 + - - +
157B LEU* 4.7 7.9 - - + +
160B ASN* 3.2 32.5 + - - +
161B GLY 3.2 20.3 + - - +
162B ILE* 3.4 13.5 - - - +
199B LEU* 3.5 19.4 - - - +
200B SER* 2.8 37.3 + - - +
202B LEU* 3.8 33.1 - - + +
222B LEU* 1.3 76.5 - - - +
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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