Contacts of the helix formed by residues 352 - 363 (chain C) in PDB entry 5L26
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 352 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313C PRO* 4.8 3.9 - - - +
316C GLU* 3.1 13.5 + - - -
351C LEU* 1.3 77.2 - - - +
353C ASP* 1.3 64.1 + - - +
354C THR* 3.3 17.9 - - - +
355C THR* 2.7 27.9 + - - -
356C LYS* 3.2 21.5 + - - +
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Residues in contact with ASP 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C TYR* 4.5 4.2 + - - +
351C LEU 4.8 2.8 - - - +
352C SER* 1.3 75.1 - - - +
354C THR* 1.3 61.7 + - - +
356C LYS* 3.5 9.6 + - - +
357C ALA* 3.2 21.3 + - - +
416C THR* 4.5 6.6 + - - +
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Residues in contact with THR 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C GLY 5.0 2.3 + - - +
313C PRO* 5.4 8.1 - - + -
352C SER* 3.3 18.4 - - - +
353C ASP* 1.3 81.1 - - - +
355C THR* 1.3 61.2 + - - +
357C ALA* 3.3 3.6 + - - +
358C ILE* 3.0 33.9 + - + +
413C GLY* 3.6 13.0 + - - -
416C THR* 3.1 35.7 + - - +
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Residues in contact with THR 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C VAL* 4.0 19.5 - - + +
313C PRO* 3.6 13.0 - - - +
316C GLU* 2.4 39.5 + - + +
320C ALA* 5.1 0.4 - - + -
351C LEU* 4.5 7.6 - - + -
352C SER* 2.7 18.7 + - - -
353C ASP 3.3 0.4 - - - -
354C THR* 1.3 76.3 - - - +
356C LYS* 1.3 60.4 - - - +
357C ALA 3.1 1.3 - - - -
358C ILE* 3.1 8.6 + - - +
359C ILE* 2.9 50.9 + - + +
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Residues in contact with LYS 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PRO* 6.2 2.0 - - + -
201C TYR* 4.2 5.6 - - + -
339C PHE* 3.7 13.0 - - + -
343C LEU* 4.3 23.3 - - + -
351C LEU* 5.2 7.1 - - + +
352C SER 3.2 13.8 + - - +
353C ASP* 3.7 9.6 - - - +
355C THR* 1.3 79.8 - - - +
357C ALA* 1.3 53.3 + - - +
359C ILE* 5.2 0.2 - - - -
360C SER* 2.4 36.0 + - - -
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Residues in contact with ALA 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C TYR* 3.5 37.8 - - + +
353C ASP 3.2 9.5 + - - +
354C THR 3.5 9.2 - - - +
355C THR 3.1 0.6 - - - -
356C LYS* 1.3 75.9 - - - +
358C ILE* 1.3 64.4 + - - +
360C SER* 3.3 1.0 + - - -
361C PHE* 3.0 30.5 + - - -
412C ALA* 4.4 12.8 - - + -
416C THR* 4.4 14.1 - - + +
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Residues in contact with ILE 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ILE* 3.8 26.2 - - + +
311C GLY* 3.3 34.1 - - - +
312C VAL* 3.7 24.2 - - + -
324C ILE* 6.1 0.2 - - + -
354C THR* 3.0 27.0 + - + +
355C THR* 3.1 8.5 + - - +
357C ALA* 1.3 76.9 - - - +
359C ILE* 1.3 60.0 + - + +
362C ALA* 3.0 23.8 + - + +
409C ALA* 3.3 25.8 - - + +
412C ALA* 4.6 0.4 - - - -
413C GLY* 3.6 24.9 - - - -
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Residues in contact with ILE 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C ILE* 5.0 0.4 - - + -
320C ALA* 3.9 24.2 - - + +
323C LEU* 3.7 23.1 - - + -
324C ILE* 5.5 3.1 - - + -
339C PHE* 3.6 38.8 - - + -
351C LEU* 4.4 9.2 - - + -
355C THR* 2.9 33.2 + - + +
358C ILE* 1.3 79.1 - - + +
360C SER* 1.3 62.4 + - - +
362C ALA* 4.4 4.9 - - - -
363C LEU* 3.0 46.4 + - + +
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Residues in contact with SER 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C VAL* 4.7 8.3 - - - -
198C PRO* 4.1 7.6 - - - +
201C TYR* 3.6 33.5 - - - +
202C LEU* 4.6 4.2 - - - +
205C ALA* 5.0 0.7 - - - +
336C TYR* 2.8 30.8 + - - -
339C PHE* 3.6 14.8 - - - -
356C LYS 2.4 24.6 + - - -
357C ALA 3.3 2.8 + - - -
359C ILE* 1.3 79.3 - - - +
361C PHE* 1.3 59.0 + - - +
364C CYS* 3.5 6.9 - - - +
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Residues in contact with PHE 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU* 3.9 15.3 - - + -
201C TYR* 3.4 46.0 - + + -
204C ALA* 3.6 17.5 - - + -
205C ALA* 3.5 38.1 - - + +
208C MET* 3.9 11.0 - - + -
357C ALA 3.0 27.0 + - - +
360C SER* 1.3 76.7 - - - +
362C ALA* 1.3 64.9 + - - +
363C LEU 3.2 1.6 - - - -
364C CYS* 3.3 17.7 + - - +
405C ASN* 3.6 14.0 - - - +
408C SER* 3.8 30.6 - - - +
409C ALA* 3.8 9.0 - - - +
412C ALA* 3.5 14.4 - - + -
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Residues in contact with ALA 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ILE* 4.9 1.1 - - + -
324C ILE* 4.1 27.6 - - + +
327C LYS* 3.3 19.4 - - - +
358C ILE 3.0 18.0 + - - +
359C ILE* 3.9 4.9 - - - +
361C PHE* 1.3 78.1 - - - +
363C LEU* 1.3 61.5 - - + +
364C CYS 3.3 0.2 - - - -
405C ASN* 3.4 23.6 - - - +
406C LEU* 4.3 10.0 - - + +
409C ALA* 3.7 12.3 - - + +
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Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C LEU* 4.0 10.1 - - + +
324C ILE* 3.7 38.6 - - + +
327C LYS* 3.6 12.5 - - + -
332C GLU* 3.7 12.6 - - - +
335C ALA* 3.7 34.5 - - + +
336C TYR* 3.2 41.5 - - + -
339C PHE* 4.4 2.7 - - + -
359C ILE* 3.0 39.8 + - + +
362C ALA* 1.3 78.4 - - + +
364C CYS* 1.3 58.8 + - - +
365C GLY 3.0 8.1 + - - -
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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