Contacts of the strand formed by residues 226 - 229 (chain A) in PDB entry 4D85
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 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASN* 1.3 70.4 - - - +
227A ARG* 1.3 65.5 + - - +
228A LEU* 3.3 33.7 - - + -
275A ILE* 5.3 8.7 - - + -
277A LEU* 5.4 7.9 - - + -
292A ILE* 4.7 7.2 - - + -
310A ALA 3.3 2.4 + - - -
311A ILE* 3.4 32.0 - - + +
312A SER 3.0 24.4 + - - +
318A THR* 4.1 8.5 - - + -
319A VAL 3.5 12.1 - - - +
320A MET* 4.8 1.1 - - + -
323A VAL* 3.1 23.1 - - + +
324A ILE* 3.5 29.6 - - + -
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Residues in contact with ARG 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 4.8 12.5 - - - +
75A GLN* 3.1 34.1 + - - +
223A THR* 3.5 17.1 - - + +
225A ASN* 4.0 11.8 - - + +
226A LEU* 1.3 74.3 - - - +
228A LEU* 1.3 61.8 + - - +
312A SER* 3.3 16.6 + - - +
313A GLN 3.9 16.8 + - - -
314A SER* 3.6 17.8 - - - +
315A SER* 5.1 8.5 + - - +
318A THR* 3.1 10.0 - - - +
319A VAL* 2.8 56.1 + - + +
401A 0GU 3.4 13.1 + - - -
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 6.5 1.8 - - + -
205A LEU* 6.2 0.2 - - + -
226A LEU* 3.3 35.9 - - + -
227A ARG* 1.3 76.8 - - - +
229A PRO* 1.3 73.4 - - + +
232A VAL* 4.1 15.0 - - + -
233A PHE* 4.0 13.8 - - + +
236A ALA* 3.9 28.0 - - + -
277A LEU* 5.6 7.0 - - + -
311A ILE* 4.0 22.4 - - + -
312A SER 3.0 4.9 + - - -
313A GLN* 3.5 4.5 - - - -
314A SER* 2.7 32.4 + - - -
318A THR* 4.1 13.2 - - + +
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Residues in contact with PRO 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU* 3.5 25.1 - - - +
212A TYR 4.0 4.0 - - - +
214A TYR* 3.7 13.0 - - + +
228A LEU* 1.3 85.6 - - + +
230A LYS* 1.3 56.1 + - - +
231A LYS* 3.4 1.6 - - + +
232A VAL* 3.0 17.6 + - + +
233A PHE 2.7 32.1 + - - -
314A SER 4.2 2.0 - - - +
316A THR 4.1 10.5 - - - +
317A GLY* 3.7 21.8 - - - -
318A THR* 3.5 20.6 - - - +
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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