Contacts of the helix formed by residues 358 - 371 (chain C) in PDB entry 5VSW
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 ASP 358 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C ARG* 3.5 17.2 - - - +
215C TYR 6.0 0.2 - - - -
216C THR* 5.9 5.8 - - + +
357C ASN* 1.3 102.6 + - - +
359C ARG* 1.3 64.3 + - - +
360C LEU* 3.0 30.1 + - - +
361C SER* 3.1 16.7 + - - -
362C ALA 3.5 10.7 + - - -
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Residues in contact with ARG 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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211C ARG 3.2 25.2 + - - +
212C ALA* 3.1 18.7 + - - +
213C LEU 4.7 0.4 - - - -
214C ASN* 4.0 32.6 - - - +
216C THR* 6.3 0.4 - - - +
358C ASP* 1.3 74.9 - - - +
360C LEU* 1.3 65.2 + - - +
362C ALA* 3.2 5.7 + - - +
363C LEU* 3.0 44.1 + - + +
378C ARG* 5.6 0.8 - - - +
382C GLU* 2.5 37.7 + - - +
385C PHE* 5.9 0.4 - - - -
386C GLU* 3.9 22.0 + - - +
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Residues in contact with LEU 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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358C ASP* 3.0 10.0 + - - +
359C ARG* 1.3 79.0 - - - +
361C SER* 1.3 61.9 + - - +
363C LEU* 4.2 19.7 - - + -
364C VAL* 3.1 40.0 + - + +
378C ARG* 3.4 58.1 - - + +
381C ALA* 5.1 2.2 - - + -
382C GLU* 4.5 9.2 - - + -
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Residues in contact with SER 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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355C PRO 4.4 1.2 + - - -
356C THR* 3.1 33.3 - - - +
357C ASN* 3.6 10.8 + - - -
358C ASP* 3.1 33.8 + - - -
359C ARG 3.1 0.4 - - - -
360C LEU* 1.3 77.7 - - - +
362C ALA* 1.3 60.6 + - - +
364C VAL* 3.6 6.1 + - - +
365C GLU* 3.3 15.4 + - - +
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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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208C ILE* 3.2 44.4 - - + +
211C ARG* 4.0 11.2 - - + -
212C ALA* 4.5 3.4 - - + +
356C THR* 3.5 14.6 - - - +
358C ASP 3.5 1.0 + - - -
359C ARG 3.2 8.0 + - - +
361C SER* 1.3 74.8 - - - +
363C LEU* 1.3 61.4 + - - +
364C VAL 3.1 1.8 - - - -
365C GLU* 2.8 18.7 + - - +
366C ILE* 2.8 20.1 + - - +
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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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212C ALA* 3.7 22.9 - - + +
359C ARG* 3.0 48.9 + - + +
360C LEU* 3.9 10.5 - - + +
362C ALA* 1.3 76.7 - - - +
364C VAL* 1.3 61.1 + - - +
366C ILE* 3.6 6.7 + - + +
367C TYR* 3.2 14.6 + - - +
381C ALA* 3.1 33.1 - - + +
382C GLU* 3.6 29.8 - - + +
384C LEU* 5.4 0.3 - - - +
385C PHE* 3.6 35.4 - - + -
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Residues in contact with VAL 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 3.1 31.6 + - + +
361C SER* 3.7 6.1 - - - +
363C LEU* 1.3 75.2 - - - +
365C GLU* 1.3 66.6 + - - +
367C TYR* 3.0 5.9 + - - +
368C ARG* 2.9 33.4 + - + +
376C PRO* 4.2 32.3 - - + +
377C THR 5.4 3.4 - - - +
381C ALA* 4.3 9.9 - - + -
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Residues in contact with GLU 365 (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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204C LEU* 3.8 18.9 - - + +
208C ILE* 3.6 27.1 - - + -
355C PRO* 3.9 22.8 - - + +
356C THR* 4.0 4.8 - - + +
361C SER 3.3 9.5 + - - +
362C ALA 2.8 11.7 + - - +
364C VAL* 1.3 80.3 - - - +
366C ILE* 1.3 60.4 + - - +
368C ARG* 3.4 30.0 + - - +
369C MET* 3.4 22.0 + - - +
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Residues in contact with ILE 366 (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 ILE* 4.4 23.1 - - + -
204C LEU* 4.5 10.1 - - + -
208C ILE* 3.6 28.3 - - + +
209C ILE* 4.8 3.1 - - + -
212C ALA* 4.3 12.3 - - + -
362C ALA 2.8 19.0 + - - +
363C LEU* 3.9 7.6 - - - +
365C GLU* 1.3 75.3 - - - +
367C TYR* 1.3 65.4 + - - +
369C MET* 3.3 2.9 + - + +
370C MET* 3.1 25.4 + - + +
384C LEU* 4.5 12.6 - - + -
385C PHE* 3.7 38.8 - - + -
388C LEU* 4.7 1.6 - - + -
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Residues in contact with TYR 367 (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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363C LEU 3.2 10.7 + - - +
364C VAL* 3.0 9.0 + - - +
366C ILE* 1.3 78.3 - - - +
368C ARG* 1.3 60.9 + - + +
370C MET* 3.4 1.1 + - - +
371C ARG* 2.9 49.2 + - + +
374C GLU* 3.0 43.5 + - + -
375C PRO 3.7 20.9 + - - -
376C PRO* 4.0 19.5 - - + -
380C ALA* 4.2 22.5 - - + +
381C ALA* 4.2 11.0 - - + -
384C LEU* 3.6 36.8 - - + +
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Residues in contact with ARG 368 (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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202C ARG* 3.2 42.0 - - - +
204C LEU* 4.8 3.2 - - - +
364C VAL* 2.9 22.3 + - + +
365C GLU* 3.4 42.6 + - - +
367C TYR* 1.3 81.0 - - + +
369C MET* 1.3 58.4 + - - +
371C ARG 4.1 5.6 - - - +
372C PRO* 3.1 34.3 - - + +
373C GLY 5.1 3.1 - - - +
374C GLU 5.4 5.8 - - - +
376C PRO* 5.8 6.5 - - + -
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Residues in contact with MET 369 (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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196C VAL 5.2 0.4 - - - +
197C ARG* 4.4 2.0 - - - -
198C ILE* 3.8 30.3 - - + +
201C ARG* 3.7 21.3 + - + -
202C ARG* 3.1 71.7 - - + +
204C LEU* 3.6 24.5 - - + -
365C GLU 3.4 19.0 + - - +
366C ILE* 3.3 4.0 + - + +
367C TYR 3.2 0.4 - - - -
368C ARG* 1.3 76.9 - - - +
370C MET* 1.3 90.4 + - - +
372C PRO* 3.6 4.9 - - - +
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Residues in contact with MET 370 (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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182C SER* 5.4 1.3 - - - +
198C ILE* 3.9 35.7 - - + -
199C ASP* 3.6 22.0 - - - +
201C ARG* 2.5 46.3 + - + +
366C ILE* 3.1 20.2 + - + +
367C TYR* 4.0 4.0 - - - +
369C MET* 1.3 95.9 - - - +
371C ARG* 1.3 67.2 + - + +
372C PRO* 3.4 0.2 - - - +
384C LEU* 4.8 14.8 - - + -
388C LEU* 5.1 10.8 - - + -
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Residues in contact with ARG 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ARG* 5.4 0.4 - - - +
367C TYR* 2.9 38.2 + - + +
368C ARG* 3.7 5.5 - - - +
370C MET* 1.3 85.6 - - + +
372C PRO* 1.3 68.4 - - - +
374C GLU* 3.8 37.9 + - + +
384C LEU* 4.8 16.8 - - + +
394C ARG* 6.1 1.2 - - - +
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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