Contacts of the strand formed by residues 403 - 410 (chain A) in PDB entry 1FO4
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 ILE 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A LEU* 4.6 1.6 - - + -
245A LEU* 4.1 25.8 - - + -
246A LEU* 4.1 7.6 - - + -
249A LYS* 4.0 27.6 - - + -
257A LEU* 3.8 22.0 - - + -
287A LEU* 4.4 6.7 - - + -
374A ILE* 3.5 5.5 - - - +
375A VAL* 2.9 54.1 + - + +
398A LEU* 4.3 1.1 - - - -
401A GLU 4.6 1.8 - - - +
402A GLU* 1.3 80.1 - - - +
404A LEU* 1.3 75.6 + - - +
405A LEU* 3.9 7.2 - - + +
3006A FAD 3.6 13.9 - - + +
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.5 4.2 - - - +
301A ALA* 3.0 7.8 - - + +
349A GLY* 3.9 18.6 - - - -
352A ILE* 3.9 23.8 - - + -
353A ILE* 4.2 14.6 - - + -
372A LEU* 3.9 29.6 - - + -
373A THR 3.8 15.3 - - - +
374A ILE* 4.1 10.1 - - + +
389A PHE* 5.8 0.7 - - + -
398A LEU* 4.1 2.8 - - + +
403A ILE* 1.3 70.7 - - - +
405A LEU* 1.3 59.0 + - - +
406A SER 3.9 7.6 - - - +
407A ILE* 3.6 25.6 - - + -
3006A FAD 2.8 40.6 + - + +
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Residues in contact with LEU 405 (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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242A LEU* 4.1 24.9 - - + -
286A GLU* 3.9 28.7 - - + +
287A LEU* 3.1 29.5 - - + +
300A GLY* 3.7 2.6 - - - -
301A ALA* 2.9 19.7 + - - -
373A THR* 2.7 22.5 + - + +
375A VAL* 3.8 22.0 - - + -
380A ARG* 3.7 38.6 - - - +
403A ILE* 3.4 5.1 + - + -
404A LEU* 1.3 73.5 - - - +
406A SER* 1.3 63.4 + - - +
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Residues in contact with SER 406 (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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286A GLU 5.3 2.0 - - - -
291A GLU* 6.1 0.9 - - - -
298A SER* 3.9 15.8 + - - -
299A PHE 3.3 15.9 - - - -
300A GLY* 4.2 2.5 - - - -
371A LYS 3.9 0.2 - - - +
372A LEU* 3.7 0.7 - - - -
373A THR* 2.8 48.6 + - - +
380A ARG* 5.5 0.9 + - - -
404A LEU* 3.7 2.2 - - - +
405A LEU* 1.3 86.5 - - - +
407A ILE* 1.3 71.5 + - - +
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Residues in contact with ILE 407 (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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297A ILE 3.7 1.6 - - - +
298A SER* 3.1 3.2 - - - -
299A PHE* 2.7 41.6 + - - +
301A ALA* 3.9 18.2 - - - -
348A LEU* 4.4 19.5 - - + -
352A ILE* 3.6 26.7 - - + -
365A PHE* 5.1 4.3 - - + -
370A THR* 3.1 32.5 - - + -
371A LYS 3.3 4.5 - - - +
372A LEU* 3.8 11.4 - - + -
404A LEU* 3.6 24.0 - - + -
406A SER* 1.3 85.8 - - - +
408A GLU* 1.3 58.6 + - - +
409A ILE* 4.0 8.9 + - + -
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Residues in contact with GLU 408 (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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293A GLY* 4.8 7.3 + - - -
294A PRO* 5.7 0.9 - - - +
295A GLU* 3.6 21.9 + - - +
296A GLY* 4.0 20.2 + - - +
297A ILE 3.3 20.4 - - - +
298A SER* 3.9 14.3 - - - +
370A THR* 3.3 4.9 - - - +
371A LYS* 2.9 55.3 + - + +
407A ILE* 1.3 73.0 - - - +
409A ILE* 1.3 63.8 + - - +
410A PRO* 3.4 6.2 - - - +
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Residues in contact with ILE 409 (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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296A GLY* 3.3 0.9 - - - -
297A ILE 2.8 36.7 + - - +
299A PHE* 3.9 25.6 - - + -
308A VAL* 4.3 7.6 - - + -
312A LEU* 3.9 19.1 - - + -
326A VAL* 3.9 15.0 - - + -
327A PHE* 3.4 30.0 - - + -
330A VAL* 4.3 10.1 - - + -
348A LEU* 5.1 2.7 - - + -
365A PHE* 4.1 25.8 - - + -
370A THR* 4.2 4.9 - - + +
407A ILE* 4.6 8.5 - - + -
408A GLU* 1.3 71.2 - - - +
410A PRO* 1.3 71.3 - - + +
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Residues in contact with PRO 410 (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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295A GLU 3.5 9.0 - - - +
296A GLY* 4.3 0.2 - - - -
323A LYS 4.8 0.2 - - - +
326A VAL* 3.7 20.4 - - + +
327A PHE* 3.4 15.2 - - - -
368A SER* 3.4 30.1 - - - +
369A GLY 4.4 2.7 - - - +
370A THR* 3.5 23.6 - - - +
371A LYS* 5.0 2.0 - - + +
408A GLU* 3.4 7.1 - - + +
409A ILE* 1.3 89.3 - - + +
411A TYR* 1.3 69.9 + - - +
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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