Contacts of the helix formed by residues 291 - 302 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274B LEU* 3.4 5.4 - - - +
278B PHE* 3.5 29.4 - - - -
289B GLY 4.0 1.0 + - - -
290B LEU* 1.3 75.1 - - - +
292B PHE* 1.3 64.3 + - - +
293B ARG* 3.4 9.7 + - - +
294B ASP* 2.9 46.5 + - - +
295B VAL 3.2 9.0 + - - -
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Residues in contact with PHE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ASP* 4.1 5.6 - - - +
287A PRO* 3.6 19.7 - - + -
288A GLY* 3.5 29.6 - - - +
274B LEU* 3.4 18.7 - - + +
278B PHE* 4.1 13.0 - - + -
291B SER* 1.3 72.6 - - - +
293B ARG* 1.3 63.2 + - - +
295B VAL* 3.0 12.8 + - - +
296B LEU* 3.1 38.7 + - + -
328B VAL* 3.6 31.2 - - + -
331B LYS* 3.6 31.0 - - + -
332B LEU* 3.6 32.8 - - + -
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ARG* 4.1 3.2 - - - +
243A MET* 3.3 41.1 - - + +
244A ARG* 3.8 15.0 - - - +
246A PHE* 5.5 3.8 - - + -
275A ASP* 5.2 0.2 + - - -
288A GLY* 2.8 40.1 + - - +
289A GLY 4.7 5.8 - - - +
103B GLU* 2.9 40.6 + - - -
291B SER* 3.2 7.3 + - - +
292B PHE* 1.3 78.9 - - - +
294B ASP* 1.3 52.5 + - - +
296B LEU* 3.2 21.8 + - - +
297B ASN* 2.8 58.7 + - - +
300B HIS* 4.4 1.0 + - - -
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Residues in contact with ASP 294 (chain B).
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* 5.8 0.2 - - - +
246B PHE* 4.0 9.9 - - + -
250B ARG* 3.1 39.3 + - - +
254B GLU* 4.6 1.3 - - - +
289B GLY 5.0 0.3 - - - +
290B LEU* 3.7 19.7 - - + -
291B SER* 2.9 45.5 + - - +
293B ARG* 1.3 75.9 - - - +
295B VAL* 1.3 61.5 + - - +
297B ASN* 3.3 11.2 + - - +
298B ILE* 3.2 28.5 + - - +
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 4.0 19.1 - - + -
269B ILE* 4.7 0.9 - - + -
273B CYS* 3.9 13.0 - - - -
274B LEU* 3.8 17.7 - - + -
290B LEU* 3.9 24.9 - - + -
291B SER 3.2 10.9 + - - +
292B PHE* 3.0 9.5 + - - +
294B ASP* 1.3 76.7 - - - +
296B LEU* 1.3 57.3 + - - +
298B ILE* 3.1 9.3 + - - +
299B LEU* 2.9 37.3 + - + +
332B LEU* 3.8 27.1 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLU* 3.5 34.3 - - - +
292B PHE* 3.1 44.0 + - + +
293B ARG* 3.2 22.0 + - - +
295B VAL* 1.3 73.7 - - - +
297B ASN* 1.3 58.9 + - - +
299B LEU* 4.3 14.8 - - + -
300B HIS* 2.7 49.7 + - + +
331B LYS* 4.2 4.5 - - - -
332B LEU* 4.7 4.9 - - + -
335B GLU* 3.9 28.5 - - + -
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Residues in contact with ASN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A MET 4.9 1.4 - - - +
244A ARG* 4.6 10.7 - - - +
247A SER* 3.2 24.8 + - - -
250B ARG* 4.3 5.9 - - - +
254B GLU* 3.0 35.6 + - + +
293B ARG* 2.8 42.9 + - - +
294B ASP* 3.6 5.3 + - - +
295B VAL 3.3 0.2 - - - -
296B LEU* 1.3 75.8 - - - +
298B ILE* 1.3 63.0 + - - +
300B HIS* 4.8 1.6 + - - -
301B ASN* 2.7 39.1 + - - +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.0 26.5 - - + -
184B LEU* 4.4 13.2 - - + -
220B VAL* 4.1 24.2 - - + -
246B PHE* 4.9 7.0 - - + -
253B LEU* 3.5 38.9 - - + +
254B GLU* 4.5 7.9 - - + +
256B LEU* 4.3 8.0 - - + +
290B LEU* 4.6 11.2 - - + -
294B ASP 3.2 19.6 + - - +
295B VAL* 3.1 9.4 + - - +
297B ASN* 1.3 78.8 - - - +
299B LEU* 1.3 58.6 + - + +
301B ASN* 3.9 0.7 - - - +
302B LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B LEU* 4.4 12.8 - - + -
184B LEU* 4.4 3.8 - - + -
267B ILE* 4.1 37.5 - - + -
269B ILE* 3.8 24.2 - - + -
295B VAL* 2.9 29.9 + - + +
296B LEU* 4.0 18.8 - - + +
298B ILE* 1.3 74.5 - - - +
300B HIS* 1.3 60.0 + - + +
301B ASN 3.3 0.5 + - - -
302B LEU* 3.4 5.2 + - + -
332B LEU* 4.6 6.7 - - + +
335B GLU* 5.1 5.4 - - + -
336B LEU* 4.3 14.8 - - + +
339B LYS* 2.8 41.9 + - + -
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Residues in contact with HIS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ARG* 3.9 19.6 + - + +
103B GLU* 3.3 33.2 - - + -
104B GLU* 4.0 35.3 + - + +
293B ARG* 4.6 1.0 + - - -
296B LEU* 2.7 39.8 + - + +
297B ASN* 4.8 1.7 + - - -
299B LEU* 1.3 77.1 - - + +
301B ASN* 1.3 68.4 + - - +
302B LEU 4.3 0.7 - - - +
335B GLU* 2.9 34.6 + - + +
339B LYS* 3.7 9.9 + - + +
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Residues in contact with ASN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ARG 5.8 2.6 + - - -
254B GLU* 3.1 29.1 + - - +
255B ASN* 4.7 3.5 - - - -
256B LEU 3.8 7.9 + - - +
297B ASN* 2.7 36.7 + - - +
299B LEU 3.2 1.0 - - - -
300B HIS* 1.3 81.6 - - - +
302B LEU* 1.3 67.9 + - - +
303B GLN* 3.2 11.6 + - - +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.2 16.4 - - + -
256B LEU* 3.4 36.5 - - + +
258B LEU* 4.0 17.7 - - + -
265B VAL* 4.7 4.5 - - + -
267B ILE* 3.8 31.9 - - + -
298B ILE 3.0 17.8 + - - +
299B LEU* 3.4 10.1 + - + +
300B HIS 4.3 0.7 - - - +
301B ASN* 1.3 77.7 - - - +
303B GLN* 1.3 69.5 + - - +
304B ALA* 3.8 18.4 + - + -
339B LYS* 3.0 24.1 + - - -
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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