Contacts of the helix formed by residues 245 - 253 (chain B) in PDB entry 5VZ4
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 TRP 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B PHE* 3.6 18.6 - + - -
241B GLN* 2.9 38.3 + - - +
244B CYS* 1.3 90.0 - - + +
246B GLN* 1.3 57.4 + - - +
247B ARG 3.3 3.1 - - - -
248B VAL* 3.2 17.4 + - + +
249B THR* 2.9 24.6 + - - -
266B ASP 6.0 0.2 - - - -
267B LEU* 3.7 13.5 - - + -
268B THR 3.6 44.6 - - - -
269B CYS* 3.6 10.3 - - + -
309B HIS* 3.7 28.0 - + - -
310B MET* 3.2 49.3 + - + +
315B SER* 4.1 8.7 - - - -
316B CYS* 3.6 20.3 - - - -
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Residues in contact with GLN 246 (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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241B GLN 3.6 1.0 + - - -
242B SER 3.7 17.4 + - - +
243B LYS 5.5 2.5 - - - +
244B CYS 3.6 3.8 + - - -
245B TRP* 1.3 73.1 - - - +
247B ARG* 1.3 78.5 + - + +
249B THR* 3.1 5.0 + - - -
250B ARG* 2.9 70.7 + - - +
268B THR 5.3 1.4 + - - -
270B SER* 5.8 5.2 - - - -
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Residues in contact with ARG 247 (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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245B TRP 3.3 0.6 - - - -
246B GLN* 1.3 89.9 + - + +
248B VAL* 1.3 63.6 + - - +
250B ARG* 3.7 10.7 - - - +
251B LYS* 3.2 31.3 + - + +
262B LEU* 5.2 0.2 - - - +
265B GLN* 3.2 26.4 + - - +
266B ASP* 3.5 28.9 + - + +
268B THR* 3.6 32.4 + - - +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLN* 3.6 21.5 - - - +
245B TRP* 3.2 18.9 + - + +
247B ARG* 1.3 77.7 - - - +
249B THR* 1.3 59.3 + - - +
251B LYS* 4.8 0.4 - - - -
252B CYS* 3.0 29.7 + - + +
253B HIS 3.8 0.8 + - - +
259B ILE* 4.3 15.0 - - + -
262B LEU* 3.6 33.4 - - + -
266B ASP 3.8 11.4 - - - +
267B LEU* 3.7 21.3 - - + -
310B MET* 4.1 16.6 - - + -
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Residues in contact with THR 249 (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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238B ARG 5.7 0.2 - - - +
241B GLN* 3.1 40.6 + - + +
242B SER* 4.5 18.4 - - - +
245B TRP 2.9 7.7 + - - -
246B GLN* 3.1 4.9 + - - -
248B VAL* 1.3 80.1 - - - +
250B ARG* 1.3 60.0 + - - +
253B HIS* 2.9 49.4 + - + +
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Residues in contact with ARG 250 (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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246B GLN* 2.9 57.1 + - - +
247B ARG* 3.7 10.3 - - - +
249B THR* 1.3 78.7 - - - +
251B LYS* 1.3 72.3 + - + +
253B HIS* 4.2 15.6 + - - -
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Residues in contact with LYS 251 (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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247B ARG* 3.2 23.4 + - + +
248B VAL 4.1 0.4 - - - +
250B ARG* 1.3 88.0 - - + +
252B CYS* 1.3 69.9 + - - +
253B HIS* 5.4 1.5 - - - -
258B CYS* 3.7 10.2 - - - -
262B LEU* 4.3 8.9 - - + +
266B ASP* 2.6 37.8 + - - +
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Residues in contact with CYS 252 (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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248B VAL 3.0 10.7 + - - +
251B LYS* 1.3 81.2 - - - +
253B HIS* 1.3 73.9 + - - +
255B ASP* 3.2 20.9 + - - +
258B CYS* 2.1 60.7 - - + +
259B ILE* 3.6 18.8 - - + -
262B LEU* 3.7 25.1 - - - -
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Residues in contact with HIS 253 (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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241B GLN* 4.4 12.3 + - - -
248B VAL 3.8 3.2 + - - +
249B THR* 2.9 40.6 + - + +
250B ARG* 4.2 14.2 + - - -
251B LYS 5.4 0.9 - - - -
252B CYS* 1.3 81.2 - - - +
254B GLU* 1.3 69.4 + - + +
255B ASP 3.4 0.4 + - - -
259B ILE* 4.0 11.8 - - - +
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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