Contacts of the helix formed by residues 361 - 368 (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 LEU 361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B LEU* 4.0 27.1 - - + -
330B VAL* 4.5 15.7 - - + -
333B GLN* 4.1 18.8 - - + -
334B LEU* 4.2 17.7 - - + -
337B PHE* 4.0 17.3 - - + -
348B LEU* 4.2 15.3 - - + -
351B ASN* 3.3 23.1 - - + +
359B SER* 3.3 1.4 + - - -
360B ASP* 1.3 84.1 - - - +
362B ASN* 1.3 61.9 + - - +
363B PRO* 3.2 2.9 - - - -
364B VAL* 2.8 23.5 + - + +
365B PHE* 2.8 30.8 + - + -
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Residues in contact with ASN 362 (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* 3.5 16.8 + - - -
352B ILE* 3.3 33.2 + - - +
355B ALA* 4.0 6.9 - - - +
356B SER 4.6 0.2 - - - +
359B SER* 3.2 21.5 + - - +
361B LEU* 1.3 77.0 - - - +
363B PRO* 1.3 63.5 - - + +
365B PHE* 4.1 5.6 - - - -
366B MET* 2.8 32.6 + - - +
385B MET* 3.5 5.6 - - - +
390B PHE* 3.4 31.5 - - + -
463B THR* 3.6 17.4 + - - +
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Residues in contact with PRO 363 (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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359B SER 3.2 25.8 - - - +
360B ASP 3.8 3.4 - - - +
361B LEU 3.3 6.3 - - - +
362B ASN* 1.3 93.8 - - + +
364B VAL* 1.3 54.6 + - - +
367B ALA* 2.9 31.0 + - - +
435B THR* 4.2 4.9 - - + -
436B CYS* 4.0 5.8 - - - -
437B GLY* 3.8 9.4 - - - +
455B CYS* 3.5 30.3 - - + +
457B GLY* 4.0 16.4 - - - +
463B THR* 3.8 21.5 - - + +
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B VAL* 4.6 5.2 - - + -
329B GLY 4.5 1.1 - - - +
330B VAL* 3.8 30.7 - - + +
333B GLN* 4.0 8.5 - - + -
360B ASP 3.8 16.2 - - - +
361B LEU* 2.8 11.3 + - + +
363B PRO* 1.3 76.8 - - - +
365B PHE* 1.3 59.7 + - + +
367B ALA 3.6 0.2 + - - -
368B SER* 2.7 34.8 + - - -
418B PHE* 3.7 24.7 - - + -
420B ALA* 4.0 26.5 - - + -
436B CYS 4.0 8.3 - - - +
437B GLY* 4.2 2.2 - - - -
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Residues in contact with PHE 365 (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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326B VAL* 6.3 0.2 - - + -
330B VAL* 4.4 13.7 - - + -
348B LEU* 3.7 26.2 - - + -
352B ILE* 3.9 37.7 - - + -
361B LEU* 2.8 44.2 + - + +
362B ASN* 4.1 3.4 - - - -
364B VAL* 1.3 80.5 - - + +
366B MET* 1.3 57.1 + - - +
369B GLY* 3.1 4.7 + - - -
370B THR* 2.8 56.6 + - + -
385B MET* 3.6 23.0 - - + +
407B ILE* 4.9 2.5 - - + -
409B ILE* 3.9 27.6 - - + -
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Residues in contact with MET 366 (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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362B ASN 2.8 18.8 + - - +
363B PRO 3.7 4.0 - - - +
365B PHE* 1.3 75.6 - - - +
367B ALA* 1.3 64.7 + - - +
369B GLY* 3.1 10.0 + - - -
385B MET* 3.4 17.2 - - - +
386B ASP* 3.5 29.2 - - - +
387B HIS* 3.9 17.0 - - - +
390B PHE* 3.5 32.8 - - + -
453B ALA* 5.2 1.2 - - - +
455B CYS* 3.5 25.6 - - + -
463B THR* 3.7 24.9 - - + +
464B ILE 4.2 3.6 - - - -
465B SER* 4.0 11.2 - - - -
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Residues in contact with ALA 367 (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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363B PRO 2.9 14.1 + - - +
364B VAL 4.1 0.2 - - - +
366B MET* 1.3 76.6 - - - +
368B SER* 1.3 58.0 + - - +
369B GLY 3.3 0.4 + - - -
418B PHE* 3.8 12.8 - - + -
437B GLY 3.1 34.5 - - - +
438B MET* 4.0 0.9 - - - +
439B ARG* 2.8 27.6 + - - +
453B ALA* 3.8 18.6 - - - +
455B CYS* 3.6 12.5 - - - -
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Residues in contact with SER 368 (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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326B VAL* 3.7 37.0 - - - +
364B VAL* 2.7 22.4 + - - +
365B PHE* 3.4 0.7 + - - -
367B ALA* 1.3 76.3 - - - +
369B GLY* 1.3 61.9 + - - +
370B THR* 2.9 21.8 + - - -
410B PRO* 3.5 15.4 - - - +
418B PHE* 4.0 4.5 - - - -
439B ARG* 4.1 14.6 + - - +
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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