Contacts of the strand formed by residues 209 - 213 (chain B) in PDB entry 3A3K
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 VAL 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B HIS* 4.1 5.6 - - + +
146B TRP* 3.7 46.7 - - + +
149B GLN 4.1 10.4 + - - +
150B ALA* 3.4 4.9 - - + +
151B LEU 3.0 23.9 + - - +
208B ARG* 1.3 79.2 + - - +
210B ILE* 1.3 59.3 + - - +
211B TYR* 3.8 22.9 - - + -
237B VAL* 3.9 14.4 - - + -
239B PHE* 4.1 3.4 - - + -
417B PRO* 5.0 2.5 - - + +
418B PRO 5.1 0.2 - - - +
419B ASP* 3.6 28.5 + - + -
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.4 26.2 - - + +
153B LEU* 4.2 17.0 - - + -
203B VAL* 4.0 5.8 - - + -
207B GLY 3.7 13.0 - - - +
208B ARG 3.4 23.3 - - - +
209B VAL* 1.3 73.9 - - - +
211B TYR* 1.3 63.9 + - - +
212B ILE* 3.8 23.1 - - + -
236B TYR* 3.7 16.2 - - + -
237B VAL 2.9 10.7 + - - +
238B PHE* 3.8 27.8 - - + -
239B PHE* 2.7 36.0 + - - +
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Residues in contact with TYR 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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137B VAL* 3.3 22.1 - - + +
140B LEU* 4.4 6.6 - - + +
141B HIS* 2.7 39.3 + - - -
150B ALA* 4.2 13.2 - - + -
151B LEU 2.8 15.0 + - - +
152B VAL* 3.2 22.5 - - + -
153B LEU 2.8 31.6 + - - -
171B LEU* 4.9 8.5 - - + -
209B VAL* 3.8 12.3 - - + -
210B ILE* 1.3 75.7 - - - +
212B ILE* 1.3 57.7 + - - +
213B CYS 4.2 0.2 - - - -
239B PHE* 3.4 44.5 - + + +
241B LEU* 4.1 22.2 - - + -
280B ILE* 4.0 12.3 - - + -
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.3 20.0 - - + +
188B PHE* 5.1 1.1 - - + -
203B VAL* 6.3 0.2 - - + -
210B ILE* 3.8 18.8 - - + -
211B TYR* 1.3 79.0 - - - +
213B CYS* 1.3 59.9 + - - +
214B SER* 3.4 26.9 - - - +
219B PHE* 3.8 35.2 - - + -
222B LEU* 4.0 25.8 - - + -
223B MET* 3.9 17.5 - - + -
238B PHE* 4.4 4.7 - - + -
239B PHE 2.9 9.1 + - - +
240B HIS* 3.3 8.0 - - - -
241B LEU* 2.8 28.1 + - - +
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Residues in contact with CYS 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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153B LEU 2.8 8.7 + - - -
154B TYR* 3.1 13.0 - - + -
155B ALA 3.0 25.3 + - - -
164B CYS* 2.1 53.6 - - + -
167B ILE* 3.8 23.8 - - - -
168B VAL* 4.5 3.8 - - + -
211B TYR 4.2 0.2 - - - -
212B ILE* 1.3 72.3 - - - +
214B SER* 1.3 60.8 + - - +
241B LEU* 4.1 27.5 - - + +
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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