Contacts of the helix formed by residues 314 - 324 (chain E) in PDB entry 5WUA
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 PHE 314 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310E ASP 4.0 1.7 + - - -
311E LEU* 3.5 23.6 + - + +
312E LEU* 3.0 0.8 - - - -
313E GLY* 1.3 75.0 - - - +
315E ALA* 1.3 65.0 + - - +
316E GLY 3.1 1.1 - - - -
317E PRO* 3.0 24.8 - - + +
318E LEU* 3.4 12.5 + - + +
444E GLN 4.3 4.7 - - - -
447E VAL* 3.0 50.0 - - + -
448E GLY* 3.4 14.1 - - - -
451E LEU* 3.4 17.5 - - + -
582E LEU* 5.6 11.4 - - + -
585E ILE* 5.9 8.1 - - + -
586E LEU* 6.2 2.9 - - + -
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Residues in contact with ALA 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E LEU* 2.7 26.2 + - + +
313E GLY 3.0 1.5 - - - +
314E PHE* 1.3 77.7 - - - +
316E GLY* 1.3 65.1 + - - +
318E LEU* 3.7 3.3 + - - +
319E CYS* 3.3 23.0 + - - +
365E ALA* 4.2 30.5 - - + +
366E LEU* 5.1 2.2 - - - +
369E GLN* 5.0 5.2 - - + -
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Residues in contact with GLY 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E GLY 3.8 6.3 + - - -
314E PHE 3.1 1.2 - - - -
315E ALA* 1.3 79.8 - - - +
317E PRO* 1.3 63.2 - - - +
319E CYS* 3.8 4.1 - - - +
320E ILE* 2.9 23.5 + - - +
581E SER* 5.0 6.5 - - - -
1289E LEU* 6.1 4.9 - - - -
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Residues in contact with PRO 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E GLY 5.1 0.2 - - - -
314E PHE* 3.0 19.9 - - + +
316E GLY* 1.3 74.7 - - - +
318E LEU* 1.3 65.4 + - - +
320E ILE* 2.9 18.9 + - + +
321E PHE* 2.9 11.8 + - - +
578E ALA* 4.8 18.3 - - + +
581E SER* 4.6 16.9 - - - -
582E LEU* 4.9 12.3 - - + +
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Residues in contact with LEU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E PHE* 3.4 10.8 + - + +
315E ALA* 4.5 2.9 - - - +
317E PRO* 1.3 79.2 - - - +
319E CYS* 1.3 64.0 + - - +
321E PHE* 2.9 19.1 + - - +
322E GLY* 2.9 11.1 + - - -
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Residues in contact with CYS 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E ALA 3.3 17.1 + - - +
316E GLY* 3.8 3.6 - - - +
317E PRO 3.3 0.2 - - - -
318E LEU* 1.3 77.3 - - - +
320E ILE* 1.3 63.4 + - - +
322E GLY* 3.1 11.5 + - - +
323E ILE* 3.1 17.8 + - - +
358E LEU* 5.3 4.3 - - + +
362E LEU* 3.9 29.4 - - + -
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Residues in contact with ILE 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E GLY 2.9 14.3 + - - +
317E PRO* 2.9 15.8 + - + +
319E CYS* 1.3 75.5 - - - +
321E PHE* 1.3 48.4 + - - +
323E ILE* 4.9 1.1 - - - +
324E VAL* 2.6 39.3 + - - +
574E SER 5.7 1.1 - - - -
577E PHE* 5.1 9.8 - - + +
578E ALA* 4.8 15.7 - - - +
581E SER* 5.5 3.8 - - - -
1285E LEU* 5.3 15.0 - - + -
1286E THR* 6.2 1.6 - - - +
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Residues in contact with PHE 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E PRO 2.9 9.9 + - - +
318E LEU* 2.9 13.9 + - - +
320E ILE* 1.3 76.9 - - - +
322E GLY* 1.3 64.5 + - - +
324E VAL* 3.2 8.2 + - - +
325E ASP* 3.2 16.6 + - - +
574E SER* 4.6 18.2 - - - +
578E ALA* 5.4 7.7 - - + +
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Residues in contact with GLY 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E LEU 2.9 12.3 + - - -
319E CYS* 3.1 3.9 + - - -
321E PHE* 1.3 76.7 - - - +
323E ILE* 1.3 57.6 + - - +
325E ASP* 2.8 29.5 + - - +
326E HIS 4.2 0.5 + - - -
358E LEU* 5.4 7.6 - - - -
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Residues in contact with ILE 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E CYS 3.1 12.4 + - - +
320E ILE* 4.9 1.6 - - - +
322E GLY* 1.3 74.7 - - - +
324E VAL* 1.3 61.7 + - - +
325E ASP 3.0 1.5 + - - -
326E HIS* 3.3 21.7 + - - +
355E ALA* 5.6 9.4 - - + +
358E LEU* 5.1 12.3 - - + +
359E ALA* 6.0 3.8 - - + +
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Residues in contact with VAL 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E ILE 2.6 26.3 + - - +
321E PHE* 3.2 12.6 - - - +
322E GLY 3.0 0.4 - - - -
323E ILE* 1.3 77.6 - - - +
325E ASP* 1.3 61.0 + - - +
326E HIS 3.7 5.4 - - - +
573E PRO* 4.8 12.3 - - + +
574E SER* 3.8 26.7 + - - +
577E PHE* 6.2 2.9 - - + -
1282E GLY* 6.6 0.2 - - - -
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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