Contacts of the helix formed by residues 352 - 365 (chain B) in PDB entry 3FO5
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 ALA 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B SER* 1.3 58.8 + - - +
354B ALA 3.6 1.3 - - - -
355B ARG* 3.8 22.2 - - - +
356B LYS* 2.6 44.6 + - + +
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Residues in contact with SER 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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352B ALA* 1.3 79.2 - - - +
354B ALA* 1.3 59.6 + - - +
356B LYS* 3.7 2.0 - - - +
357B LYS* 2.9 30.7 + - - +
563B ALA* 3.1 25.7 + - - +
564B GLY* 4.5 5.5 + - - -
565B LEU* 3.7 18.5 - - - +
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Residues in contact with ALA 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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353B SER* 1.3 78.9 - - - +
355B ARG* 1.3 67.2 + - + +
357B LYS* 3.3 7.3 + - - +
358B ILE* 3.1 36.7 + - + +
565B LEU* 4.2 11.4 - - + +
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Residues in contact with ARG 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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352B ALA* 3.8 22.2 - - - +
353B SER 3.2 0.4 - - - -
354B ALA* 1.3 79.0 - - + +
356B LYS* 1.3 65.4 + - - +
358B ILE* 3.2 8.3 + - - +
359B ARG* 2.9 24.2 + - - +
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Residues in contact with LYS 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ALA* 2.6 27.3 + - + +
353B SER* 3.7 3.6 - - - +
355B ARG* 1.3 73.5 - - - +
357B LYS* 1.3 62.2 + - - +
359B ARG* 3.4 29.6 + - - +
360B LEU* 3.0 40.7 + - + +
407B SER* 4.2 16.4 + - - +
419B GLU* 5.6 3.6 - - - -
562B VAL* 2.7 36.1 + - - +
563B ALA* 4.0 12.9 - - + +
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Residues in contact with LYS 357 (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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353B SER 2.9 13.5 + - - +
354B ALA* 3.5 9.6 - - - +
355B ARG 3.2 0.2 - - - -
356B LYS* 1.3 77.2 - - - +
358B ILE* 1.3 61.2 + - + +
360B LEU* 3.4 5.1 + - - +
361B ASP* 2.4 69.1 + - - +
556B ASN* 3.1 20.6 + - - -
559B THR* 3.5 19.5 + - - +
560B THR* 3.2 27.1 - - - +
563B ALA* 3.7 14.1 - - + +
565B LEU* 3.7 25.6 - - + -
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Residues in contact with ILE 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ALA* 3.1 25.7 + - + +
355B ARG* 3.8 5.8 - - - +
357B LYS* 1.3 78.5 - - + +
359B ARG* 1.3 60.5 + - - +
361B ASP* 3.4 11.9 + - + +
362B ARG* 2.9 61.7 + - + +
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Residues in contact with ARG 359 (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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355B ARG 2.9 16.1 + - - +
356B LYS* 3.7 32.0 + - - +
358B ILE* 1.3 77.2 - - - +
360B LEU* 1.3 73.4 + - - +
362B ARG* 3.3 7.3 + - - +
363B LYS* 2.8 40.7 + - + +
419B GLU* 3.8 23.8 + - - -
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Residues in contact with LEU 360 (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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356B LYS* 3.0 37.5 + - + +
357B LYS* 3.8 3.4 - - - +
359B ARG* 1.3 86.1 - - - +
361B ASP* 1.3 68.2 + - - +
363B LYS* 3.2 4.1 + - + -
364B TYR* 2.9 41.3 + - + +
419B GLU* 3.7 33.9 - - - +
424B LEU* 4.3 13.0 - - + -
559B THR* 4.0 22.7 - - + +
562B VAL* 3.8 30.7 - - + -
563B ALA 4.9 0.7 - - - +
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Residues in contact with ASP 361 (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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357B LYS* 2.4 51.3 + - - +
358B ILE* 3.5 12.0 - - + +
359B ARG 3.3 0.2 - - - -
360B LEU* 1.3 74.8 - - - +
362B ARG* 1.3 59.0 + - + +
365B ILE* 2.9 41.3 + - + +
555B LEU* 5.0 6.4 - - - +
556B ASN* 4.8 5.3 - - - -
559B THR* 2.7 30.2 + - - +
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Residues in contact with ARG 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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358B ILE* 2.9 44.1 + - + +
359B ARG* 3.7 6.3 - - - +
361B ASP* 1.3 75.2 - - + +
363B LYS* 1.3 61.3 + - - +
365B ILE* 3.9 15.2 - - - +
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Residues in contact with LYS 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 ARG* 2.8 27.8 + - + +
360B LEU* 3.6 5.8 - - + +
361B ASP 3.2 0.4 - - - -
362B ARG* 1.3 78.3 - - - +
364B TYR* 1.3 102.4 + - + +
365B ILE 3.7 2.4 - - - +
419B GLU* 3.7 23.6 + - - +
420B ASP 4.6 4.2 + - - -
421B ASP* 5.6 4.5 - - - +
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Residues in contact with TYR 364 (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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360B LEU* 2.9 40.3 + - + +
363B LYS* 1.3 111.1 - - + +
365B ILE* 1.3 66.1 + - - +
366B VAL 3.7 7.1 + - - +
419B GLU* 2.9 32.1 - - + +
420B ASP 3.0 26.7 + - - -
421B ASP 4.8 3.1 - - - -
422B LYS 4.0 15.0 - - - +
423B PHE* 3.5 17.5 - - - -
424B LEU* 3.8 30.1 - - + +
555B LEU* 3.2 29.0 - - + +
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Residues in contact with ILE 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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361B ASP* 2.9 22.7 + - + +
362B ARG* 3.9 14.3 - - - +
363B LYS 4.8 2.6 - - - +
364B TYR* 1.3 76.8 - - - +
366B VAL* 1.3 87.2 + - + +
555B LEU* 3.6 15.2 - - + +
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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