Contacts of the strand formed by residues 209 - 213 (chain B) in PDB entry 4K8T
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 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B VAL* 5.1 3.8 - - + -
180B GLU* 4.6 13.2 - - + +
181B MSE 3.1 3.0 + - - -
182B SER* 2.9 36.3 + - - +
183B MSE 3.0 12.5 + - - -
207B VAL* 3.6 1.9 - - - +
208B ASP* 1.3 86.9 - - + +
210B VAL* 1.3 67.1 + - - +
211B PHE* 4.2 13.7 - - + -
239B ILE* 3.2 34.1 - - + +
241B ALA 5.3 1.6 - - - +
282B PHE* 4.5 10.1 - - + -
283B LEU* 5.0 6.3 - - + -
286B TYR* 3.6 43.7 - - + +
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Residues in contact with VAL 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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183B MSE 3.4 9.2 - - + +
185B LEU* 4.2 20.4 - - + -
202B MSE 3.6 33.4 - - + -
207B VAL* 3.6 21.1 - - + -
209B ILE* 1.3 76.7 - - - +
211B PHE* 1.3 70.1 + - - +
212B ALA 4.3 0.2 + - - -
233B ILE* 4.3 9.6 - - + +
237B CYS* 3.6 23.8 - - + -
239B ILE 2.9 7.5 + - - -
240B ALA* 3.3 3.2 - - + +
241B ALA* 2.8 32.9 + - - +
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Residues in contact with PHE 211 (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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152B TYR* 3.6 20.9 - + - +
182B SER* 3.3 27.4 - - - -
183B MSE 2.8 12.2 + - - +
184B THR* 3.4 14.2 + - - +
185B LEU* 3.0 30.7 + - - +
209B ILE* 4.2 7.4 - - + -
210B VAL* 1.3 74.4 - - - +
212B ALA* 1.3 61.8 + - - +
241B ALA* 3.4 18.8 - - + -
243B THR* 6.0 0.2 - - + -
275B GLY 5.7 0.2 - - - -
278B PHE* 3.8 20.4 - + - -
279B ALA* 3.8 16.4 - - + -
282B PHE* 3.7 42.0 - + + -
283B LEU* 3.9 18.2 - - + -
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Residues in contact with ALA 212 (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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185B LEU* 3.5 24.2 - - + -
210B VAL 5.6 0.2 - - - +
211B PHE* 1.3 75.5 - - - +
213B ASN* 1.3 67.8 + - - +
216B GLU* 3.3 9.0 - - + +
217B ALA* 4.4 6.5 - - + +
233B ILE* 4.1 17.7 - - + -
241B ALA 3.1 7.7 + - - +
242B VAL* 3.2 10.4 - - + -
243B THR* 2.8 26.0 + - - +
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Residues in contact with ASN 213 (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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212B ALA* 1.3 74.7 - - - +
214B ARG* 1.3 63.2 + - - +
215B GLN* 3.3 26.0 + - - +
216B GLU* 2.8 51.8 + - - +
217B ALA* 3.0 21.7 + - - +
242B VAL* 4.4 2.5 - - - -
243B THR* 3.3 23.8 - - - +
244B MSE 5.9 0.2 - - - -
245B SER* 6.0 2.2 - - - +
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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