Contacts of the strand formed by residues 213 - 218 (chain B) in PDB entry 5U03
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 LEU 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ASN 3.3 5.0 + - - +
178B ILE* 3.7 15.0 - - + +
179B HIS 3.1 22.9 + - - -
211B PRO* 3.7 2.9 - - - +
212B ASP* 1.4 87.9 - - + +
214B VAL* 1.3 64.3 + - - +
215B VAL 4.0 0.6 + - - -
239B GLU* 4.7 2.5 - - + +
240B GLN* 3.7 24.5 - - - -
242B ILE* 3.7 25.1 - - + -
262B VAL* 4.6 7.9 - - + -
265B TYR* 3.6 39.0 - - + -
266B PHE* 3.6 35.2 - - + -
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B HIS* 3.2 18.2 - - + +
181B SER* 4.6 0.9 - - - -
197B THR* 4.5 18.6 - - + -
201B VAL* 4.7 8.1 - - + -
211B PRO* 3.6 25.4 - - + -
212B ASP 5.6 0.2 - - - -
213B LEU* 1.3 77.6 - - - +
215B VAL* 1.3 69.7 + - - +
216B CYS* 3.6 13.8 + - - -
230B ILE* 5.9 2.7 - - + -
234B CYS* 5.3 7.6 - - + -
236B VAL* 5.0 18.2 - - + -
240B GLN 3.0 13.3 + - - +
241B VAL* 5.2 2.9 - - + -
242B ILE* 3.0 27.9 + - - +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.2 27.8 - - + -
178B ILE* 3.9 26.0 - - + -
179B HIS 2.7 7.3 + - - +
180B VAL* 3.9 22.4 - - + -
181B SER* 2.8 27.9 + - - -
213B LEU 4.0 0.2 - - - -
214B VAL* 1.3 76.0 - - - +
216B CYS* 1.3 66.4 + - - +
217B ARG* 4.6 0.9 - - - +
242B ILE* 3.8 17.5 - - + -
244B VAL* 3.6 28.7 - - + -
257B LEU* 6.0 2.2 - - + -
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Residues in contact with CYS 216 (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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181B SER 4.1 4.0 - - - -
183B VAL* 3.8 19.3 - - + -
197B THR* 5.3 7.2 - - - -
214B VAL* 3.9 19.3 - - - -
215B VAL* 1.3 80.6 - - - +
217B ARG* 1.3 59.9 + - - +
218B CYS* 3.0 12.5 + - - -
222B LEU* 4.6 1.3 - - + -
230B ILE* 4.6 13.7 - - - -
241B VAL* 4.2 21.1 - - - -
242B ILE 2.7 21.7 + - - +
243B CYS* 4.2 0.4 - - - -
244B VAL* 2.8 30.1 + - - +
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Residues in contact with ARG 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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186A PRO* 5.4 3.8 - - - +
188A SER* 3.1 28.9 + - - -
13B GLY 3.2 18.2 + - - -
14B ILE* 2.6 49.3 + - + +
180B VAL* 5.1 2.0 - - + -
181B SER 2.9 21.9 + - - +
182B LEU* 3.6 16.3 - - + +
183B VAL* 2.7 32.6 + - - +
215B VAL* 3.9 3.1 + - + +
216B CYS* 1.3 70.1 - - - +
218B CYS* 1.3 56.8 + - - +
244B VAL* 3.7 5.8 - - - -
246B ASP* 2.8 28.0 + - - +
601B ATP 3.4 43.2 + - - -
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Residues in contact with CYS 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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182B LEU* 6.2 0.2 - - - -
183B VAL* 4.2 7.4 - - - -
216B CYS* 3.0 19.0 + - - -
217B ARG* 1.3 74.8 - - - +
219B SER* 1.3 60.6 + - - +
220B ASN 3.2 11.9 - - - +
222B LEU* 3.5 19.7 - - + -
243B CYS* 2.1 51.4 - - - -
244B VAL 3.0 6.3 + - - +
245B HIS* 3.5 4.9 - - - -
246B ASP* 3.0 29.7 + - - +
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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