Contacts of the helix formed by residues 347 - 355 (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 SER 347 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B VAL* 3.7 19.9 - - - +
301B ALA 3.3 14.3 + - - -
302B ALA* 3.7 17.3 - - - -
303B CYS 3.3 6.5 - - - -
304B ALA* 4.3 0.2 - - - +
305B LEU* 4.1 5.0 - - - +
345B VAL 3.5 0.2 + - - -
346B ALA* 1.3 73.2 - - - +
348B LEU* 1.3 63.0 + - - +
350B GLY* 3.1 15.9 + - - -
351B ASN* 3.3 16.5 + - - +
4006B FAD 2.8 32.8 + - - -
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Residues in contact with LEU 348 (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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299B PHE* 3.6 35.0 - - + -
300B GLY 4.4 3.1 - - - +
301B ALA 3.4 4.9 + - - +
303B CYS 3.1 10.4 + - - +
305B LEU* 3.9 18.1 - - + +
308B VAL* 3.7 29.6 - - + -
330B VAL* 6.3 0.4 - - + -
347B SER* 1.3 71.1 - - - +
349B GLY* 1.3 66.5 + - - +
351B ASN* 3.3 4.6 + - - +
352B ILE* 3.1 28.8 + - + +
361B LEU* 4.2 4.7 - - + -
365B PHE* 3.7 30.5 - - + -
407B ILE* 4.2 27.1 - - + -
409B ILE* 5.0 2.7 - - + -
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Residues in contact with GLY 349 (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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301B ALA* 2.7 29.1 + - - +
348B LEU* 1.3 74.6 - - - +
350B GLY* 1.3 61.4 + - - +
353B ILE* 2.9 30.5 + - - +
404B LEU* 3.8 23.8 - - - -
407B ILE* 4.6 0.2 - - - +
4006B FAD 4.2 11.0 - - - -
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Residues in contact with GLY 350 (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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347B SER* 3.1 13.9 + - - -
348B LEU 3.2 0.2 - - - -
349B GLY* 1.3 76.7 - - - +
351B ASN* 1.3 56.3 + - - +
354B THR* 2.8 35.3 + - - -
4006B FAD 3.3 47.5 - - - +
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Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 5.4 0.4 - - + -
337B PHE* 3.7 3.6 - - - -
347B SER 3.3 7.1 + - - +
348B LEU 3.3 8.3 + - - +
350B GLY* 1.3 77.6 - - - +
352B ILE* 1.3 63.7 + - + +
354B THR* 3.6 3.3 + - - -
355B ALA 3.6 8.5 + - - -
356B SER 4.8 0.3 + - - -
359B SER* 2.8 27.3 + - - -
361B LEU* 3.3 38.7 - - + +
362B ASN* 3.5 12.2 + - - +
4006B FAD 2.9 58.8 + - - +
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Residues in contact with ILE 352 (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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348B LEU* 3.1 16.6 + - + +
349B GLY 3.9 2.7 - - - +
351B ASN* 1.3 77.7 - - + +
353B ILE* 1.3 64.1 + - + +
355B ALA* 3.3 14.4 + - - +
362B ASN* 3.3 15.8 + - - +
365B PHE* 3.9 28.7 - - + -
372B LEU* 4.0 10.1 - - + -
385B MET* 3.9 19.3 - - + -
389B PHE* 3.9 17.7 - - + -
390B PHE* 3.7 11.8 - - + -
396B THR* 4.0 1.0 - - - +
404B LEU* 3.9 16.8 - - + -
407B ILE* 3.5 32.5 - - + -
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Residues in contact with ILE 353 (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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349B GLY 2.9 18.3 + - - +
352B ILE* 1.3 81.0 - - + +
354B THR* 1.3 66.9 + - - +
355B ALA* 2.9 8.4 + - - +
389B PHE* 4.5 4.5 - - + -
394B ARG 4.4 5.2 - - - +
396B THR* 4.0 20.0 - - + +
398B LEU* 3.6 34.8 - - + -
404B LEU* 4.5 9.9 - - + -
4006B FAD 3.5 49.7 + - + +
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Residues in contact with THR 354 (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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263B GLU* 3.2 37.2 - - + +
267B GLU* 5.4 0.4 - - - +
350B GLY 2.8 25.4 + - - -
351B ASN 3.8 5.4 - - - -
352B ILE 3.4 0.2 - - - -
353B ILE* 1.3 77.0 - - - +
355B ALA* 1.3 67.9 + - - +
356B SER* 3.8 15.9 - - - +
394B ARG* 3.6 40.7 + - - +
4006B FAD 3.7 21.6 + - - +
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Residues in contact with ALA 355 (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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351B ASN 3.6 2.6 + - - -
352B ILE 3.3 9.2 + - - -
353B ILE 2.9 9.2 - - - +
354B THR* 1.3 80.7 - - - +
356B SER* 1.3 66.3 + - - +
357B PRO* 3.7 3.5 - - - +
362B ASN* 4.0 9.2 - - - +
390B PHE* 3.7 28.8 - - + -
394B ARG* 3.8 28.5 + - - -
395B LYS 4.1 1.1 - - - +
396B THR* 3.8 9.9 - - + -
461B ASP 5.2 1.0 - - - +
462B ARG* 5.4 3.3 - - - +
463B THR* 5.8 0.6 + - - -
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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