Contacts of the strand formed by residues 213 - 216 (chain I) in PDB entry 5FUR
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 213 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I MET* 1.3 80.3 - - - +
214I ALA* 1.3 73.5 + - - +
215I VAL* 5.7 2.9 - - + -
232I LYS* 5.3 7.6 - - - +
234I PHE* 4.0 20.0 - - + -
250I ALA 4.0 0.7 - - - +
252I GLY* 3.1 26.8 + - - +
253I PRO 3.2 14.5 + - - +
254I PHE* 3.6 23.3 - - + +
256I ILE* 5.7 1.3 - - + -
268I PHE* 4.1 24.0 - - + -
305I LYS* 5.1 9.6 - - + +
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Residues in contact with ALA 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206I PHE* 3.5 32.5 - - + -
208I VAL* 4.3 7.4 - - + -
213I VAL* 1.3 82.8 - - - +
215I VAL* 1.3 69.2 + - - +
234I PHE* 3.9 9.2 - - + -
236I TYR* 3.0 19.5 + - - -
249I LEU* 4.5 0.7 - - + -
250I ALA 3.1 11.7 - - - +
251I ILE* 4.0 14.4 - - + -
305I LYS* 5.9 0.3 + - - -
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Residues in contact with VAL 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213I VAL* 5.7 3.6 - - + +
214I ALA* 1.3 81.4 - - - +
216I SER* 1.3 60.7 + - - +
236I TYR* 4.2 3.1 - - - -
248I SER 3.8 0.7 - - - +
249I LEU* 3.3 9.2 - - - -
250I ALA* 2.8 52.7 + - + +
305I LYS* 5.5 4.0 - - + +
307I VAL* 5.8 9.0 - - + -
324I ILE* 3.1 30.0 - - + +
327I THR* 3.3 35.7 - - + +
329I LEU* 6.5 0.4 - - + -
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Residues in contact with SER 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I TRP* 4.7 2.8 - - - -
204I LEU* 3.1 36.0 - - - +
215I VAL* 1.3 77.2 - - - +
217I ASN* 1.3 81.3 + - - +
218I GLY 5.2 1.1 - - - -
236I TYR* 3.4 19.2 - - - -
247I ILE* 4.8 5.2 - - - +
248I SER 3.1 16.6 + - - -
249I LEU* 4.7 3.1 - - - -
324I ILE* 3.8 5.7 - - - +
325I PHE* 3.5 20.4 + - - +
327I THR* 4.4 1.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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