Contacts of the helix formed by residues 350 - 360 (chain B) in PDB entry 3F9C
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 VAL 350 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319B SER* 3.3 12.6 - - - -
321B TYR* 4.3 18.8 - - + -
348B GLY 4.4 2.5 - - - +
349B SER* 1.3 78.0 - - - +
351B HIS* 1.3 67.5 + - - +
352B GLN 3.1 6.4 + - - +
353B ASN* 2.7 38.0 + - - +
354B PHE* 4.5 1.0 - - - -
367B HIS* 6.4 0.4 - - + -
370B LYS* 3.8 31.6 - - + +
372B LYS 3.6 32.8 - - - +
373B GLY* 4.2 5.8 - - - -
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Residues in contact with HIS 351 (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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272B HIS* 2.9 33.3 + + - -
273B SER* 2.8 35.7 + - - -
296B ASP* 2.6 47.4 + - - +
319B SER* 3.4 4.2 + - - -
322B PHE* 3.3 37.7 - + + +
350B VAL* 1.3 75.5 - - - +
352B GLN* 1.3 68.5 + - + +
353B ASN 3.2 1.4 + - - -
354B PHE* 3.5 8.8 + - - -
473B DFP 3.4 29.9 + - + -
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Residues in contact with GLN 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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272B HIS* 4.5 1.4 - - - -
350B VAL* 3.1 2.2 + - - +
351B HIS* 1.3 83.2 - - + +
353B ASN* 1.3 63.2 + - - +
354B PHE 3.1 4.2 + - - -
355B ALA* 3.1 40.6 + - - +
357B PHE* 4.5 14.7 - - - +
358B THR* 3.6 6.4 + - - +
370B LYS 3.5 24.0 - - - +
371B LEU* 3.9 26.7 - - + +
473B DFP 3.7 37.1 - - - +
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Residues in contact with ASN 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 SER* 3.2 18.1 - - - -
350B VAL* 2.7 47.2 + - - +
352B GLN* 1.3 76.9 - - - +
354B PHE* 1.3 64.8 + - + +
355B ALA 3.7 0.8 + - - +
358B THR* 3.6 29.5 + - - +
371B LEU 4.2 0.2 + - - -
373B GLY* 3.7 12.1 + - - +
375B ILE* 4.1 4.1 - - - +
377B SER* 3.8 15.9 + - - +
380B ALA* 4.0 22.3 - - + +
381B ILE* 3.8 17.5 + - - +
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Residues in contact with PHE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B TYR* 3.8 6.6 - - - +
162B ALA* 5.8 0.3 - - - +
163B ILE* 3.4 32.4 - - + +
272B HIS* 3.5 32.1 - + + -
295B LEU* 4.0 14.8 - - + -
296B ASP* 3.7 19.5 - - + -
317B ILE* 3.6 30.3 - - + -
318B ASN 3.7 14.6 - - - -
319B SER* 3.8 16.8 - - - -
346B ILE* 4.5 7.6 - - + -
349B SER* 5.2 1.6 - - - -
350B VAL 4.5 2.5 - - - -
351B HIS 3.6 12.8 - - - -
352B GLN 3.1 1.2 - - - -
353B ASN* 1.3 82.6 - - + +
355B ALA* 1.3 59.3 + - - +
356B ASP* 5.1 0.9 - - - +
359B PHE* 5.9 0.2 - - - -
381B ILE* 4.0 7.5 - - + +
384B SER* 3.4 32.3 - - - -
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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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159B LEU* 3.7 11.4 - - + +
160B TYR* 3.6 26.5 - - + +
272B HIS* 4.6 6.1 - - + +
352B GLN* 3.1 34.2 + - - +
354B PHE* 1.3 77.7 - - - +
356B ASP* 1.3 67.4 + - - +
357B PHE* 3.3 5.4 + - + +
358B THR* 3.3 15.1 - - - +
359B PHE* 4.2 1.7 - - - -
473B DFP 5.5 1.8 - - + -
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Residues in contact with ASP 356 (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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56B ILE* 3.9 10.6 - - + +
97B TRP* 3.2 32.3 + - + +
159B LEU* 2.8 27.9 + - - +
160B TYR* 3.9 1.6 - - - -
161B SER* 2.6 39.1 + - - -
162B ALA* 3.1 29.1 + - - +
354B PHE 5.1 0.7 - - - +
355B ALA* 1.3 70.6 - - - +
357B PHE* 1.3 56.5 + - - +
358B THR 3.1 6.3 - - - -
359B PHE* 3.0 29.1 + - - +
360B ALA* 3.7 3.5 + - - +
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Residues in contact with PHE 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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97B TRP* 3.7 27.6 - + - -
98B ILE* 3.9 13.7 - - + -
104B PHE* 5.2 0.9 - + - -
107B LEU* 4.1 22.0 - - + -
121B LEU* 5.5 4.9 - - + -
125B PHE* 3.9 31.9 - + - -
159B LEU* 4.1 29.6 - - + -
352B GLN* 4.5 10.8 - - - +
355B ALA* 3.3 4.2 + - + +
356B ASP* 1.3 72.1 - - - +
358B THR* 1.3 59.3 + - - +
359B PHE 3.0 6.1 + - - -
360B ALA* 3.3 22.4 + - + +
361B THR* 4.3 2.1 + - - -
371B LEU* 3.6 44.8 - - + +
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Residues in contact with THR 358 (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 GLN* 3.6 11.9 + - - +
353B ASN* 3.6 21.1 + - - +
355B ALA 3.3 16.6 + - - +
356B ASP 3.1 0.8 - - - -
357B PHE* 1.3 78.1 - - - +
359B PHE* 1.3 83.1 + - + +
360B ALA 3.5 0.2 - - - -
361B THR 5.2 0.2 - - - -
371B LEU* 2.4 33.2 + - - +
372B LYS* 2.8 32.8 + - - +
377B SER* 2.7 26.6 + - - +
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Residues in contact with PHE 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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55B LYS* 2.8 57.4 - - - +
56B ILE* 4.1 9.6 - - + -
57B PRO* 3.6 21.1 - - + -
162B ALA* 3.6 21.1 - - + -
353B ASN 5.1 0.9 - - - -
355B ALA 4.2 5.8 - - - -
356B ASP* 3.0 20.3 + - - +
358B THR* 1.3 95.2 - - + +
360B ALA* 1.3 57.0 + - - +
361B THR 3.5 5.2 - - - +
372B LYS* 4.8 2.2 - - - +
377B SER* 3.9 26.2 - - - -
378B ASN* 3.6 22.9 - - - -
381B ILE* 3.7 29.4 - - + -
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Residues in contact with ALA 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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55B LYS* 4.8 6.6 - - - +
56B ILE* 6.3 0.9 - - + -
97B TRP* 3.8 29.2 - - + -
125B PHE* 3.2 35.1 - - + -
128B MET* 4.2 16.6 - - - +
356B ASP 3.7 1.5 + - - +
357B PHE* 3.3 18.7 + - + +
358B THR 3.5 0.2 - - - -
359B PHE* 1.3 77.0 - - - +
361B THR* 1.3 59.8 + - + +
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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