Contacts of the strand formed by residues 245 - 251 (chain A) in PDB entry 6F0X
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 ALA 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A TYR* 3.5 4.5 - - - -
206A TYR* 2.6 20.9 - - + +
207A GLY* 3.5 13.7 - - - -
208A GLN* 5.0 2.9 - - + +
239A LEU 4.8 3.4 - - - +
242A ASP* 2.7 50.2 + - + +
244A ASP* 1.3 77.7 - - - +
246A LEU* 1.3 60.3 + - - +
247A VAL* 4.5 3.8 - - + +
292A ASN* 3.4 14.0 + - - -
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Residues in contact with LEU 246 (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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127A LEU* 4.0 3.4 - - + +
157A LEU* 3.8 18.4 - - + -
196A LEU 5.1 1.8 - - - +
197A THR* 5.3 2.7 - - - -
200A LEU* 3.6 33.7 - - + -
204A TYR* 3.5 39.0 - - + +
206A TYR 2.9 7.3 + - - +
207A GLY* 3.2 20.7 - - - -
208A GLN 3.5 3.3 + - - -
245A ALA* 1.3 73.2 - - - +
247A VAL* 1.3 63.0 + - - +
248A PHE* 3.5 39.0 - - + -
292A ASN* 3.2 25.6 - - + +
294A VAL* 4.9 0.9 - - + -
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Residues in contact with VAL 247 (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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208A GLN* 4.1 7.0 - - + +
236A ILE* 5.7 1.1 - - + -
239A LEU* 4.5 5.2 - - + +
240A ILE* 3.6 50.9 - - + +
245A ALA* 4.5 5.2 - - + +
246A LEU* 1.3 72.8 - - - +
248A PHE* 1.3 76.3 + - - +
249A VAL* 4.1 20.9 - - + -
292A ASN* 3.0 26.6 + - - +
293A VAL* 4.0 13.2 - - + -
294A VAL* 3.1 23.7 + - - +
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Residues in contact with PHE 248 (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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127A LEU* 4.4 9.0 - - + -
193A ALA* 3.4 24.5 - - + -
196A LEU* 3.6 38.1 - - + -
197A THR* 3.9 15.7 - - - -
208A GLN 3.0 21.6 + - - +
209A LEU* 3.1 33.2 - - + +
210A ILE* 3.4 5.4 + - - +
246A LEU* 3.5 45.8 - - + -
247A VAL* 1.3 86.4 - - - +
249A VAL* 1.3 63.8 + - - +
294A VAL* 3.3 36.1 - - + -
296A LEU* 4.9 2.9 - - + -
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Residues in contact with VAL 249 (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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209A LEU* 4.0 1.8 - - - -
210A ILE* 4.4 7.6 - - + +
212A ILE* 3.5 29.4 - - + -
236A ILE* 4.9 11.7 - - + -
247A VAL* 4.1 16.6 - - + -
248A PHE* 1.3 79.3 - - - +
250A LEU* 1.3 67.7 + - - +
251A ILE* 4.4 7.9 - - + -
287A ILE* 4.6 20.0 - - + -
293A VAL* 4.9 2.2 - - + -
294A VAL 2.6 16.8 + - - +
295A ILE* 4.2 13.7 - - + -
296A LEU* 2.8 32.7 + - - +
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A TRP* 5.6 2.0 - - + -
186A THR* 4.7 11.2 - - + +
189A CYS* 4.4 14.4 - - + -
190A LYS* 4.0 33.9 - - + -
209A LEU* 4.2 15.5 - - + +
210A ILE 3.6 11.9 + - - +
211A GLU* 4.9 12.1 - - + -
212A ILE* 3.4 21.5 + - - +
249A VAL* 1.3 75.8 - - - +
251A ILE* 1.3 82.8 + - - +
252A ASP* 3.9 13.4 + - + +
296A LEU* 3.6 24.2 - - + +
298A THR* 4.6 9.9 - - + -
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Residues in contact with ILE 251 (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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212A ILE* 3.7 39.3 - - + +
214A SER* 5.9 4.0 - - - -
249A VAL* 4.4 6.7 - - + -
250A LEU* 1.3 87.5 - - - +
252A ASP* 1.3 62.1 + - - +
253A GLN 3.3 16.6 + - - +
254A VAL* 4.2 3.1 - - - +
257A LEU* 3.7 32.3 - - + -
280A VAL* 6.2 2.7 - - + -
284A ILE* 5.8 6.1 - - + -
295A ILE* 5.0 5.2 - - + -
296A LEU 2.8 16.8 + - - +
297A THR* 3.7 16.8 - - + -
298A THR* 2.9 26.4 + - - +
309A PHE* 5.7 0.7 - - + -
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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