Contacts of the strand formed by residues 219 - 224 (chain B) in PDB entry 3ER8
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 MET 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A TYR* 4.4 24.2 - - + -
220A ARG* 3.8 6.1 - - - +
221A LEU* 3.2 46.7 + - + +
222A THR* 5.1 0.4 - - - -
164B ILE* 4.4 13.7 - - + -
191B PRO* 4.3 7.9 - - + -
214B TYR* 3.5 38.6 - - + -
216B GLY 4.2 4.2 + - - +
217B GLU 3.9 1.4 - - - -
218B ASN* 1.3 75.3 - - - +
220B ARG* 1.3 93.9 + - - +
221B LEU* 3.3 23.8 - - + -
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Residues in contact with ARG 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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219A MET 3.8 8.7 - - - +
220A ARG* 4.6 17.0 - - + +
192B HIS* 3.1 61.5 + - + +
213B ILE 4.3 7.7 + - - -
214B TYR* 5.7 3.2 - - - +
215B THR* 4.1 14.5 + - - +
218B ASN* 3.5 23.4 + - + +
219B MET* 1.3 100.9 - - - +
221B LEU* 1.3 64.2 + - - +
222B THR* 6.0 0.2 - - + -
368C SER* 3.6 23.6 + - - -
372C ASP* 5.3 1.0 + - - -
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Residues in contact with LEU 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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218A ASN* 3.9 0.5 - - - +
219A MET* 2.9 42.5 + - + +
221A LEU* 3.7 33.0 - - + -
161B ASN* 4.0 17.3 - - + +
189B TYR* 3.9 25.8 - - + -
190B ILE 3.5 4.7 - - - +
191B PRO* 4.0 11.7 - - + -
192B HIS 4.4 0.2 - - - +
219B MET* 3.3 33.7 - - + -
220B ARG* 1.3 74.4 - - - +
222B THR* 1.3 71.2 + - - +
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Residues in contact with THR 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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217A GLU* 3.0 15.3 - - - +
218A ASN* 3.6 14.6 - - + +
189B TYR* 3.9 2.9 - - - -
190B ILE* 3.0 36.1 + - - +
191B PRO 4.1 5.9 + - - -
192B HIS* 4.5 24.9 - - + -
195B LYS* 5.3 7.9 + - - +
221B LEU* 1.3 80.5 - - - +
223B ARG* 1.3 64.9 + - - +
224B VAL* 3.4 7.5 + - - +
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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
----------------------------------------------------------
125A LYS* 5.0 4.0 - - - +
165A SER 3.1 23.0 + - - -
166A ILE 4.5 3.8 + - - -
168A ASN* 2.6 36.2 - - - +
216A GLY 3.7 13.9 - - - +
217A GLU* 3.1 32.6 + - - +
187B ASP* 3.5 35.4 + - + +
188B PHE 3.4 8.7 - - - +
189B TYR* 2.5 58.4 + - + -
222B THR* 1.3 70.5 - - - +
224B VAL* 1.3 68.0 + - - +
225B THR* 4.3 5.1 - - + +
228B ASP* 3.5 11.8 - - - +
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Residues in contact with VAL 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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176B TRP* 3.7 30.5 - - + -
178B CYS* 3.9 12.8 - - - -
184B TRP* 3.9 1.0 - - + -
187B ASP* 3.2 25.6 - - - +
188B PHE* 2.6 51.4 + - + +
190B ILE* 3.8 13.5 - - + -
222B THR* 3.8 11.4 - - - +
223B ARG* 1.3 74.0 - - - +
225B THR* 1.3 70.8 + - - +
228B ASP* 4.0 9.6 - - + -
232B TYR* 4.7 2.0 - - + -
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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