Contacts of the strand formed by residues 267 - 272 (chain A) in PDB entry 5FWU
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 MET 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ILE* 4.7 1.7 - - - +
265A ALA 3.7 2.9 + - - +
266A ASP* 1.3 75.6 - - - +
268A VAL* 1.3 64.9 + - - +
269A GLU* 3.7 17.5 - - + +
281A ARG* 3.1 46.0 - - + -
282A PHE 2.8 22.7 - - - +
283A HIS* 3.8 26.2 - - + +
303A PHE* 3.5 3.3 - - - -
304A PHE* 2.6 65.9 + - + -
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Residues in contact with VAL 268 (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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256A PHE* 4.7 10.3 - - + -
259A PHE* 4.4 14.6 - - + -
261A ILE* 4.7 3.8 - - + -
267A MET* 1.3 73.2 - - - +
269A GLU* 1.3 63.4 + - - +
281A ARG* 3.4 2.8 - - - -
282A PHE* 2.8 58.4 + - + -
301A LEU* 3.9 26.2 - - + -
302A TYR 3.4 4.9 - - - +
303A PHE* 3.5 28.5 - - + -
314A PHE* 4.1 21.1 - - + -
316A VAL* 6.5 0.2 - - + -
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Residues in contact with GLU 269 (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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267A MET* 3.7 23.9 - - + +
268A VAL* 1.3 75.0 - - - +
270A LEU* 1.3 63.2 + - - +
271A LEU* 3.9 21.3 - - + +
278A VAL* 4.1 13.9 - - + +
280A ALA 3.3 7.2 - - - +
281A ARG* 4.6 2.7 - - + +
282A PHE* 6.0 0.7 - - - -
300A ILE 4.4 0.2 - - - -
301A LEU* 3.5 8.0 - - - +
302A TYR* 2.7 53.8 + - + +
304A PHE* 3.5 34.2 - - + -
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Residues in contact with LEU 270 (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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244A ILE* 5.5 0.7 - - + -
254A PHE* 3.9 34.3 - - + -
256A PHE* 5.3 5.2 - - + -
269A GLU* 1.3 72.5 - - - +
271A LEU* 1.3 59.6 + - - +
278A VAL* 3.6 1.6 - - - -
279A LEU* 2.7 34.4 + - + -
280A ALA* 2.9 22.6 + - + +
282A PHE* 5.9 2.0 - - + -
292A PHE* 3.1 40.4 - - + -
294A VAL* 4.7 3.1 - - + -
299A VAL* 3.8 15.3 - - + -
300A ILE 3.5 8.3 - - - +
301A LEU* 3.4 32.5 - - + -
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Residues in contact with LEU 271 (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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269A GLU* 3.9 22.0 - - - +
270A LEU* 1.3 78.5 - - - +
272A ASP* 1.3 63.9 + - - +
276A HIS* 3.8 29.4 - - + +
277A ARG 3.5 3.4 - - - +
278A VAL* 3.2 44.2 - - + +
279A LEU* 4.0 1.6 - - - -
299A VAL* 3.1 8.3 - - - +
300A ILE* 2.9 48.9 + - + +
302A TYR* 4.9 12.1 - - + -
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Residues in contact with ASP 272 (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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271A LEU* 1.3 69.0 - - - +
273A GLY* 1.3 55.8 + - - +
274A TYR* 2.5 37.2 + - - +
275A THR* 2.7 34.3 + - - +
276A HIS* 2.8 34.8 + - - -
277A ARG* 2.9 18.4 + - + +
279A LEU* 3.6 15.4 - - + +
296A LEU* 3.3 41.8 - - + +
298A PHE 4.2 0.2 - - - -
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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
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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