Contacts of the helix formed by residues 291 - 302 (chain C) in PDB entry 6VSU
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 291 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C LEU* 3.3 7.0 - - - +
278C PHE* 3.4 27.3 - - - -
289C GLY 4.2 0.6 + - - -
290C LEU* 1.3 75.6 - - - +
292C PHE* 1.3 64.3 + - - +
293C ARG* 3.5 8.2 + - - +
294C ASP* 3.0 38.7 + - - +
295C VAL* 3.2 17.0 + - - +
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Residues in contact with PHE 292 (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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275B ASP* 4.2 5.4 + - - +
287B PRO* 3.7 17.3 - - + -
288B GLY* 3.6 27.6 - - - +
274C LEU* 3.5 17.6 - - + +
278C PHE* 4.1 13.4 - - + -
291C SER* 1.3 75.0 - - - +
293C ARG* 1.3 61.8 + - - +
295C VAL* 3.1 3.9 + - - +
296C LEU* 3.0 46.6 + - + +
328C VAL* 3.5 37.9 - - + -
331C LYS* 3.6 33.9 - - + -
332C LEU* 3.6 27.6 - - + -
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Residues in contact with ARG 293 (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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223B ARG* 3.9 4.6 - - - +
243B MET* 3.4 43.9 - - + +
244B ARG* 3.8 12.9 - - - +
246B PHE* 5.4 4.3 - - + -
275B ASP* 5.2 0.6 + - - -
288B GLY* 2.8 43.7 + - - +
289B GLY 4.9 5.8 - - - +
103C GLU* 2.7 44.6 + - - -
291C SER* 3.2 7.0 + - - +
292C PHE* 1.3 76.9 - - - +
294C ASP* 1.3 65.6 + - - +
296C LEU* 3.2 21.6 + - - +
297C ASN* 2.9 46.3 + - - +
300C HIS* 4.4 0.8 + - - -
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Residues in contact with ASP 294 (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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243C MET* 5.9 0.2 - - - +
246C PHE* 4.1 12.9 - - + -
250C ARG* 2.7 43.2 + - - +
254C GLU* 4.9 0.9 - - - +
289C GLY 5.1 0.5 - - - +
290C LEU* 3.8 18.5 - - + -
291C SER* 3.0 46.8 + - - +
293C ARG* 1.3 75.8 - - - +
295C VAL* 1.3 61.6 + - - +
297C ASN* 3.2 9.6 + - - +
298C ILE* 3.2 29.2 + - - +
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Residues in contact with VAL 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C LEU* 4.4 14.6 - - + -
269C ILE* 5.0 1.8 - - + -
273C CYS* 4.0 12.1 - - - -
274C LEU* 3.7 16.8 - - + -
290C LEU* 3.8 25.6 - - + -
291C SER 3.2 12.3 + - - +
292C PHE* 3.1 9.6 + - - +
294C ASP* 1.3 76.4 - - - +
296C LEU* 1.3 63.6 + - - +
298C ILE* 3.2 10.3 + - - +
299C LEU* 3.0 33.8 + - + +
332C LEU* 3.7 28.9 - - + -
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Residues in contact with LEU 296 (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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103C GLU* 3.3 31.6 - - - +
292C PHE* 3.0 46.3 + - + +
293C ARG* 3.2 28.9 + - - +
295C VAL* 1.3 77.1 - - - +
297C ASN* 1.3 54.4 + - - +
299C LEU* 4.5 13.2 - - + -
300C HIS* 2.8 48.0 + - + +
331C LYS* 4.2 4.5 - - - -
332C LEU* 4.6 4.9 - - + -
335C GLU* 3.9 28.3 - - + -
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Residues in contact with ASN 297 (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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243B MET 4.7 2.6 - - - +
244B ARG* 4.9 8.1 - - - +
247B SER* 3.3 24.7 + - - -
250C ARG* 4.2 7.1 - - - +
254C GLU* 3.6 31.8 + - - +
293C ARG* 2.9 42.1 + - - +
294C ASP* 3.2 9.1 + - - +
296C LEU* 1.3 73.6 - - - +
298C ILE* 1.3 62.1 + - - +
300C HIS* 4.9 3.6 + - - -
301C ASN* 3.2 35.8 + - - +
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Residues in contact with ILE 298 (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 LEU* 4.1 25.1 - - + -
184C LEU* 4.4 15.0 - - + -
220C VAL* 4.1 24.5 - - + -
246C PHE* 4.8 9.9 - - + -
253C LEU* 3.6 36.9 - - + +
254C GLU* 4.5 9.8 - - + +
256C LEU* 4.6 7.5 - - + +
290C LEU* 4.6 8.5 - - + -
294C ASP 3.2 17.7 + - - +
295C VAL* 3.2 9.5 + - - +
297C ASN* 1.3 73.2 - - - +
299C LEU* 1.3 60.8 + - - +
301C ASN* 3.3 1.6 + - - +
302C LEU* 3.0 30.2 + - + +
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Residues in contact with LEU 299 (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 LEU* 4.6 7.9 - - + -
184C LEU* 4.3 10.1 - - + -
267C ILE* 4.3 17.5 - - + -
269C ILE* 4.0 25.1 - - + -
295C VAL* 3.0 31.7 + - + +
296C LEU* 4.0 17.0 - - + +
298C ILE* 1.3 74.1 - - + +
300C HIS* 1.3 65.2 + - + +
301C ASN 3.2 0.7 + - - -
302C LEU* 3.6 4.3 + - + -
332C LEU* 4.5 7.6 - - + +
335C GLU* 5.0 3.1 - - + -
336C LEU* 4.2 33.0 - - + +
339C LYS* 3.0 37.0 + - + +
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Residues in contact with HIS 300 (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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244B ARG* 3.9 23.2 + - + +
103C GLU* 3.4 31.2 - - + +
104C GLU* 4.0 32.8 + - + +
293C ARG* 4.4 0.4 + - - -
296C LEU* 2.8 38.7 + - + +
297C ASN* 4.2 4.4 + - - +
299C LEU* 1.3 77.4 - - + +
301C ASN* 1.3 64.4 + - - +
335C GLU* 2.8 32.0 + - + +
339C LYS* 3.9 9.6 + - - +
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Residues in contact with ASN 301 (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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254C GLU* 2.7 43.1 + - - +
255C ASN* 4.8 6.6 + - - +
256C LEU 4.0 5.4 + - - +
257C LYS* 5.8 0.7 - - - -
297C ASN* 3.2 21.2 + - - +
298C ILE 4.1 0.7 - - - +
299C LEU 3.2 0.8 - - - -
300C HIS* 1.3 83.9 - - - +
302C LEU* 1.3 66.6 + - - +
303C GLN* 3.3 8.5 + - - +
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Residues in contact with LEU 302 (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 LEU* 3.6 31.0 - - + -
256C LEU* 3.3 33.8 - - + +
258C LEU* 4.0 18.4 - - + +
265C VAL* 5.0 1.8 - - + -
267C ILE* 4.0 23.1 - - + -
298C ILE* 3.0 18.0 + - + +
299C LEU* 3.6 9.3 + - + +
301C ASN* 1.3 73.8 - - - +
303C GLN* 1.3 76.2 - - - +
304C ALA* 3.8 15.9 + - + -
339C LYS* 2.8 36.5 + - - -
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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