Contacts of the strand formed by residues 205 - 210 (chain B) in PDB entry 3ELP
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 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.8 25.8 - - + -
100B LEU* 4.4 6.1 - - + -
183B ILE* 3.7 22.4 - - + -
184B LEU 3.2 3.3 + - - +
185B VAL* 3.3 19.0 - - + +
186B VAL* 2.7 34.1 + - - +
199B LEU* 4.3 1.8 - - - -
203B ALA* 4.2 2.6 - - - +
204B ASP* 1.3 83.4 - - - +
206B SER* 1.3 60.2 + - - +
225B VAL* 3.6 29.2 - - + -
226B SER 3.8 4.5 - - - +
227B VAL* 3.4 13.7 - - + -
232B LEU* 3.7 21.8 - - + -
236B LEU* 4.6 4.5 - - + -
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Residues in contact with SER 206 (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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79B ASP* 4.2 13.0 + - - +
186B VAL 3.5 4.7 - - - -
188B ASN* 3.7 11.8 + - - +
198B PRO* 3.5 36.4 - - - +
199B LEU* 4.0 18.7 - - - +
205B ILE* 1.3 73.6 - - - +
207B MET* 1.3 60.0 + - - +
208B TYR* 3.9 1.6 + - - +
224B LEU 3.8 1.6 - - - +
226B SER* 3.1 38.3 + - - -
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Residues in contact with MET 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLY* 3.5 15.0 - - - +
93B ALA* 4.0 17.3 - - + -
94B THR* 3.2 26.7 - - - +
97B ILE* 4.4 15.0 - - + -
155B TRP* 3.6 19.5 - - + -
185B VAL* 4.5 2.9 - - + -
186B VAL 2.9 12.3 + - - +
187B ASP* 3.4 27.7 - - - +
188B ASN* 2.9 24.8 + - - -
205B ILE 4.0 0.8 - - - -
206B SER* 1.3 70.9 - - - +
208B TYR* 1.3 62.0 + - - +
209B SER* 3.6 26.2 - - - -
224B LEU 3.4 9.2 - - - +
225B VAL* 4.1 7.0 - - + +
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Residues in contact with TYR 208 (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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75B VAL* 5.6 2.2 - - + -
79B ASP* 5.0 11.2 - - - +
188B ASN* 3.5 22.2 - - + -
189B THR* 3.7 21.3 + - + +
192B SER* 3.6 25.9 - - - -
193B PRO* 3.8 28.9 - - + -
206B SER 3.9 2.2 + - - +
207B MET* 1.3 71.9 - - - +
209B SER* 1.3 61.1 + - - +
210B ALA* 4.0 21.8 + - + +
214B MET* 5.9 3.6 - - - +
223B GLY* 3.8 0.3 - - - -
224B LEU* 2.8 62.9 + - + +
259B LEU* 5.4 11.0 - - + -
262B LEU* 4.6 12.8 - - + +
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLY* 3.1 34.6 + - - -
187B ASP* 5.2 0.7 - - - -
189B THR* 2.9 43.1 + - - +
207B MET* 3.6 12.1 - - - -
208B TYR* 1.3 76.6 - - - +
210B ALA* 1.3 61.6 + - - +
211B THR* 4.1 8.0 + - - +
222B MET 3.6 4.7 + - - -
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Residues in contact with ALA 210 (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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189B THR* 5.3 0.9 - - - -
208B TYR* 4.0 25.7 + - + +
209B SER* 1.3 75.4 + - - +
211B THR* 1.3 66.4 + - - +
214B MET* 6.0 5.6 - - + -
220B VAL* 3.8 2.8 - - + +
221B VAL* 3.6 4.7 - - - +
222B MET* 3.0 40.7 + - + +
224B LEU* 6.2 2.2 - - + +
255B CYS* 5.9 5.4 - - - -
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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