Contacts of the helix formed by residues 355 - 368 (chain F) in PDB entry 5U0A
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 355 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327E GLU 3.8 8.3 - - - -
328E VAL* 3.2 16.8 - - - +
330E PRO* 3.9 18.4 - - - +
338F ALA* 4.2 2.6 - - - +
353F TYR* 3.2 2.4 - - - +
354F ASP* 1.3 82.6 - - - +
356F TYR* 1.3 63.1 + - - +
357F PRO* 4.0 3.1 - - - +
358F ALA* 3.1 24.5 + - - +
359F LEU* 3.0 27.5 + - - +
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Residues in contact with TYR 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325E LEU* 6.2 0.2 - - + -
328E VAL* 3.1 29.7 + - + +
329E TRP* 3.7 29.8 - + + -
264F LEU* 4.0 22.9 - - + -
280F LEU* 4.7 8.5 - - + -
281F PRO* 2.5 46.3 + - + +
282F ASP 3.9 10.0 + - - -
283F LEU 4.1 1.4 + - - -
284F VAL* 3.4 33.9 - - + -
338F ALA* 3.6 18.4 + - + -
340F VAL* 4.4 3.5 + - + +
355F SER* 1.3 71.4 - - - +
357F PRO* 1.3 67.3 - - + +
359F LEU* 3.1 6.4 + - - +
360F ILE* 2.9 34.4 + - + +
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Residues in contact with PRO 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E VAL 4.2 3.8 - - - +
329E TRP* 4.6 8.3 - - + -
330E PRO* 4.2 13.9 - - + -
261F ARG* 4.0 23.3 - - - +
355F SER* 3.7 11.0 - - - +
356F TYR* 1.3 94.0 - - + +
358F ALA* 1.3 55.6 + - - +
360F ILE* 3.9 9.2 - - + +
361F ASP* 2.9 41.0 + - - +
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Residues in contact with ALA 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F TYR* 4.3 13.4 - - + -
354F ASP* 5.0 3.1 - - + +
355F SER* 3.1 28.2 + - - +
356F TYR 3.2 0.6 - - - -
357F PRO* 1.3 79.0 - - - +
359F LEU* 1.3 57.6 + - - +
361F ASP* 3.5 5.0 + - - +
362F ALA* 2.9 30.5 + - - +
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Residues in contact with LEU 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F LEU* 6.0 0.4 - - + -
284F VAL* 3.4 33.9 - - + +
286F ILE* 3.9 20.2 - - + -
336F GLY 3.7 19.1 - - - +
337F TYR* 3.9 16.6 - - - +
338F ALA* 3.9 2.2 - - + +
353F TYR* 3.6 35.4 - - + +
355F SER 3.0 13.8 + - - +
356F TYR 3.5 7.0 - - - +
358F ALA* 1.3 74.9 - - - +
360F ILE* 1.3 66.6 + - + +
362F ALA* 3.2 1.2 + - - -
363F MET* 2.9 36.6 + - + +
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Residues in contact with ILE 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E TRP* 6.4 0.7 - - + -
257F ALA* 3.9 23.8 - - + +
260F LEU* 3.8 13.9 - - + -
261F ARG* 3.6 36.6 - - + +
264F LEU* 3.9 17.5 - - + -
286F ILE* 3.9 23.1 - - + -
356F TYR* 2.9 24.2 + - + +
357F PRO* 3.9 7.2 - - + +
359F LEU* 1.3 75.7 - - + +
361F ASP* 1.3 61.6 + - - +
363F MET* 4.3 0.2 - - - +
364F VAL* 2.9 41.3 + - + +
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Residues in contact with ASP 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F ARG* 5.0 1.0 + - - -
257F ALA* 5.1 7.8 - - - +
357F PRO* 2.9 25.8 + - - +
358F ALA* 3.9 5.8 - - - +
360F ILE* 1.3 82.6 - - - +
362F ALA* 1.3 58.5 + - - +
364F VAL* 4.3 2.6 - - - +
365F ALA* 2.9 32.1 + - - +
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Residues in contact with ALA 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353F TYR* 3.6 37.2 - - + +
358F ALA 2.9 18.3 + - - +
359F LEU 3.2 3.6 + - - +
361F ASP* 1.3 79.3 - - - +
363F MET* 1.3 60.1 + - + +
365F ALA* 3.8 4.1 - - - +
366F ALA* 2.9 27.0 + - - +
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Residues in contact with MET 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 5.6 1.7 - - + +
260F LEU* 5.6 0.2 - - + -
286F ILE* 3.7 32.3 - - + +
288F VAL* 3.7 15.0 - - + +
334F ILE* 4.0 28.0 - - + +
335F ARG 3.5 26.2 - - - +
353F TYR* 3.4 42.8 - - + +
359F LEU* 2.9 30.2 + - + +
360F ILE 4.3 1.1 - - - +
362F ALA* 1.3 77.5 - - + +
364F VAL* 1.3 66.1 + - + +
366F ALA* 3.1 5.3 + - + +
367F ALA* 3.1 18.2 + - - +
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Residues in contact with VAL 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 5.9 2.7 - - + -
253F ARG* 3.8 43.0 + - + +
256F VAL* 4.0 20.2 - - + -
257F ALA* 4.0 27.6 - - + +
260F LEU* 4.2 9.0 - - + -
360F ILE* 2.9 26.4 + - + +
361F ASP* 4.3 3.1 - - - +
363F MET* 1.3 76.1 - - - +
365F ALA* 1.3 63.1 + - - +
367F ALA* 3.0 6.6 + - + +
368F PHE* 3.0 24.3 + - - +
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Residues in contact with ALA 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F ARG* 3.6 24.4 - - - +
361F ASP 2.9 21.5 + - - +
362F ALA* 3.9 4.0 - - - +
364F VAL* 1.3 78.3 - - - +
366F ALA* 1.3 58.7 + - - +
367F ALA 3.4 0.5 + - - -
368F PHE* 3.7 26.1 + - - +
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Residues in contact with ALA 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F VAL* 4.7 3.5 - - + +
290F PHE* 5.3 2.9 - - - -
334F ILE* 3.6 48.0 - - + +
362F ALA 2.9 18.8 + - - +
363F MET* 3.4 10.1 - - + +
364F VAL 3.1 0.4 - - - -
365F ALA* 1.3 76.8 - - - +
367F ALA* 1.3 57.3 + - - +
368F PHE* 4.6 8.2 - - - -
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Residues in contact with ALA 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F THR 6.1 0.4 - - - +
4F VAL* 4.3 6.5 - - + -
239F LEU* 3.7 28.4 - - + +
288F VAL* 3.8 19.3 - - + -
290F PHE* 6.1 2.2 - - + -
363F MET 3.1 11.7 + - - +
364F VAL* 3.0 7.3 + - - +
366F ALA* 1.3 80.6 - - - +
368F PHE* 1.3 75.0 + - - +
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Residues in contact with PHE 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239F LEU* 5.1 9.4 - - - +
243F VAL* 6.4 1.6 - - - -
249F ALA* 5.1 9.9 - - - +
253F ARG* 4.1 37.8 - - - +
256F VAL* 6.2 0.2 - - - +
364F VAL* 3.0 14.2 + - - +
365F ALA* 3.7 18.2 + - - -
366F ALA* 4.6 7.4 - - - -
367F ALA* 1.3 86.4 - - - +
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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