Contacts of the strand formed by residues 289 - 293 (chain A) in PDB entry 4FXF
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 GLY 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A ILE 3.3 3.2 + - - -
268A ILE* 3.4 15.7 - - - -
269A SER 2.9 22.0 + - - -
284A LEU* 5.3 0.2 - - - -
287A SER* 3.3 11.7 - - - -
288A ASP* 1.3 80.5 - - - +
290A ILE* 1.3 65.5 + - - +
322A LYS* 4.6 6.9 - - - +
323A PRO* 3.3 15.3 - - - -
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE* 3.5 9.2 - - - +
269A SER* 3.4 9.6 - - - +
271A ILE* 3.9 12.3 - - + -
280A PHE* 3.7 35.2 - - + -
283A ILE* 3.9 26.0 - - + -
284A LEU* 3.8 18.6 - - + -
287A SER* 4.5 0.4 - - - +
289A GLY* 1.3 82.2 - - - +
291A MET* 1.3 72.8 + - - +
292A VAL* 4.3 1.8 - - + +
313A MET* 4.5 5.8 - - + -
317A CYS* 3.8 20.2 - - - -
323A PRO 3.0 6.9 + - - +
324A VAL* 3.3 11.1 - - + +
325A ILE* 2.9 24.1 + - - +
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Residues in contact with MET 291 (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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113A ASP* 4.5 1.6 - - - +
241A PHE* 3.4 43.3 - - + -
268A ILE* 3.6 8.6 - - + +
269A SER 3.0 7.7 + - - -
270A LYS* 3.6 34.8 - - + -
271A ILE* 3.0 27.0 + - - -
290A ILE* 1.3 78.6 - - - +
292A VAL* 1.3 67.5 + - - +
293A ALA* 3.0 8.8 + - - +
325A ILE* 3.5 20.2 - - + +
327A ALA* 3.9 18.8 - - + -
328A THR* 5.9 0.2 - - - -
360A MET* 3.6 25.4 - - + -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ILE 4.3 2.5 - - - -
290A ILE* 4.7 0.7 - - + -
291A MET* 1.3 69.7 - - - +
293A ALA* 1.3 58.0 + - - +
294A ARG* 3.2 26.2 + - + +
297A LEU* 4.2 8.7 - - + -
310A GLN* 4.1 28.7 - - + +
313A MET* 3.7 46.0 - - + -
314A ILE* 4.7 2.2 - - + -
324A VAL* 4.2 13.5 - - + -
325A ILE 2.7 17.7 + - - +
326A CYS* 4.5 5.4 - - - -
327A ALA* 3.2 22.3 + - - +
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Residues in contact with ALA 293 (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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270A LYS* 4.1 21.3 - - + -
271A ILE 3.3 7.4 + - - +
272A GLU* 3.4 35.1 - - + +
291A MET* 3.0 16.8 + - - -
292A VAL* 1.3 68.6 - - - +
294A ARG* 1.3 62.9 + - - +
295A GLY 3.2 4.2 + - - -
296A ASP 3.8 1.1 + - - +
297A LEU* 3.2 22.4 + - - +
327A ALA* 4.7 0.4 - - - -
328A THR* 4.5 6.5 - - - +
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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