Contacts of the strand formed by residues 403 - 410 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B LEU* 4.7 1.1 - - + -
245B LEU* 4.1 19.1 - - + -
246B LEU* 3.9 15.3 - - + -
249B LYS* 3.9 27.4 - - + -
257B LEU* 3.7 25.6 - - + -
287B LEU* 4.3 7.4 - - + -
374B ILE* 3.6 1.6 - - - -
375B VAL* 3.0 54.2 + - + -
398B LEU* 4.3 4.9 - - - -
401B GLU 4.9 0.7 - - - +
402B GLU* 1.3 81.4 - - - +
404B LEU* 1.3 73.6 + - - +
405B LEU* 3.9 6.7 - - + +
4006B FAD 3.6 13.2 - - + +
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B LEU* 3.5 4.2 - - - +
301B ALA* 3.0 16.8 - - + +
349B GLY* 3.8 20.4 - - - -
352B ILE* 3.9 26.2 - - + -
353B ILE* 4.5 11.4 - - + -
372B LEU* 3.9 24.9 - - + -
373B THR 3.6 16.2 - - - +
374B ILE* 4.1 9.0 - - + +
389B PHE* 5.9 0.7 - - + -
398B LEU* 4.1 5.2 - - + +
403B ILE* 1.3 69.9 - - - +
405B LEU* 1.3 58.5 + - - +
406B SER 3.9 11.7 - - - +
407B ILE* 3.7 24.9 - - + -
4006B FAD 2.9 30.4 + - + +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.1 24.9 - - + -
286B GLU* 3.8 32.4 - - + +
287B LEU* 3.6 18.6 - - + +
300B GLY* 3.7 3.6 - - - -
301B ALA* 2.9 20.9 + - - +
373B THR* 2.8 21.5 + - + +
375B VAL* 3.8 27.4 - - + -
380B ARG* 3.8 34.5 - - - +
403B ILE* 3.3 3.3 + - + -
404B LEU* 1.3 72.3 - - - +
406B SER* 1.3 66.3 + - - +
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Residues in contact with SER 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B GLU 5.2 2.2 - - - -
298B SER* 3.9 15.5 + - - -
299B PHE 3.2 15.7 - - - -
300B GLY* 4.4 1.8 - - - -
371B LYS 3.9 0.2 - - - +
372B LEU* 3.7 1.0 - - - -
373B THR* 2.9 49.8 + - - +
380B ARG* 5.4 1.7 + - - -
404B LEU* 3.8 2.1 - - - +
405B LEU* 1.3 86.9 - - - +
407B ILE* 1.3 71.1 + - - +
408B GLU 4.4 0.2 - - - -
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Residues in contact with ILE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE 3.8 0.9 - - - +
298B SER* 3.2 2.6 - - - -
299B PHE* 2.7 42.6 + - - +
301B ALA* 3.7 27.1 - - - -
348B LEU* 4.2 22.0 - - + -
352B ILE* 3.5 26.5 - - + -
365B PHE* 4.9 4.5 - - + -
370B THR* 3.2 31.0 - - + -
371B LYS 3.3 4.5 - - - +
372B LEU* 3.9 9.9 - - + -
404B LEU* 3.7 17.7 - - + -
406B SER* 1.3 82.3 - - - +
408B GLU* 1.3 59.2 + - - +
409B ILE* 4.0 10.2 + - + -
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Residues in contact with GLU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B GLY* 4.8 6.6 - - - -
294B PRO* 5.8 0.3 - - - +
295B GLU* 3.7 17.3 + - - +
296B GLY* 3.9 28.0 + - - +
297B ILE 3.4 15.5 - - - +
298B SER* 4.1 13.5 - - - +
370B THR* 3.2 16.7 - - - +
371B LYS* 2.8 51.9 + - + +
407B ILE* 1.3 74.3 - - - +
409B ILE* 1.3 62.6 + - - +
410B PRO* 3.4 5.6 - - + +
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Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B GLY* 4.3 0.4 - - - -
297B ILE 2.8 37.9 + - - +
299B PHE* 4.1 24.7 - - + -
308B VAL* 4.4 7.9 - - + -
312B LEU* 4.2 16.4 - - + -
326B VAL* 3.8 20.0 - - + -
327B PHE* 3.3 33.4 - - + -
330B VAL* 4.2 10.3 - - + -
348B LEU* 5.0 2.9 - - + -
365B PHE* 3.9 29.4 - - + -
370B THR* 4.3 3.8 - - + +
407B ILE* 4.5 8.3 - - + -
408B GLU* 1.3 72.7 - - - +
410B PRO* 1.3 61.7 - - + +
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Residues in contact with PRO 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B GLU* 3.6 12.8 - - + +
296B GLY* 4.1 0.4 - - - -
326B VAL* 3.5 23.7 - - + +
327B PHE* 3.6 9.5 - - - -
368B SER* 3.5 31.9 - - - +
369B GLY 5.1 0.9 - - - +
370B THR* 3.6 17.5 - - - +
371B LYS* 5.1 0.7 - - - +
408B GLU* 3.4 11.4 - - + +
409B ILE* 1.3 88.7 - - + +
411B TYR* 1.3 68.4 + - - +
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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