Contacts of the helix formed by residues 246 - 258 (chain H) in PDB entry 3SRF
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 LYS 246 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244H ILE* 3.4 8.8 - - - +
245H ARG* 1.3 93.3 - - + +
247H ALA* 1.3 66.5 + - - +
248H SER* 3.4 19.7 - - - +
249H ASP* 3.3 40.7 + - - +
250H VAL* 3.8 0.5 + - - +
274H GLU* 4.5 12.0 + - - +
278H ARG* 4.0 18.2 - - - +
281H GLU* 3.6 11.9 - - - +
282H ILE* 3.6 12.5 - - - +
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Residues in contact with ALA 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H LYS* 1.3 70.2 - - - +
248H SER* 1.3 62.2 + - - +
250H VAL* 3.1 17.2 + - - +
251H HIS* 3.1 29.9 + - + -
281H GLU* 2.8 54.5 + - + +
282H ILE* 4.4 3.1 - - - -
285H ALA* 4.2 4.2 - - + +
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Residues in contact with SER 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H LYS* 3.4 23.3 - - - +
247H ALA* 1.3 75.1 - - - +
249H ASP* 1.3 64.1 + - - +
251H HIS* 3.1 15.4 + - - +
252H GLU* 2.9 28.7 + - - +
281H GLU* 4.8 0.2 + - - -
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Residues in contact with ASP 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H ALA* 3.3 29.3 - - + +
220H VAL* 4.5 1.0 - - - +
243H PHE 4.2 0.9 - - - +
244H ILE* 3.8 21.1 - - + -
245H ARG* 3.1 29.5 + - - +
246H LYS* 3.3 36.7 + - - +
247H ALA 3.2 0.2 - - - -
248H SER* 1.3 80.2 + - - +
250H VAL* 1.3 60.9 + - - +
252H GLU* 3.3 8.5 + - - +
253H VAL* 3.2 26.9 + - - +
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Residues in contact with VAL 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H ILE* 3.8 19.5 - - + -
246H LYS 4.1 2.7 - - - +
247H ALA* 3.1 12.2 + - - +
249H ASP* 1.3 74.8 - - - +
251H HIS* 1.3 59.2 + - + +
253H VAL* 3.4 7.7 + - - +
254H ARG* 3.0 33.4 + - - +
266H ILE* 4.3 14.6 - - + +
268H SER* 3.5 12.1 - - - +
282H ILE* 4.1 4.3 - - + -
285H ALA* 3.4 39.7 - - + +
286H SER* 3.4 24.0 - - - +
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Residues in contact with HIS 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H ALA* 3.1 30.6 + - + -
248H SER* 3.1 16.3 + - - +
250H VAL* 1.3 78.5 - - + +
252H GLU* 1.3 56.1 + - - +
254H ARG* 3.4 11.7 + - + +
255H LYS* 3.0 30.0 + - - +
284H GLU* 5.4 3.5 + - - -
285H ALA* 4.3 17.1 - - + +
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Residues in contact with GLU 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H ALA* 6.1 1.1 - - + -
220H VAL* 3.6 28.9 - - + +
225H ILE* 5.5 4.5 - - - +
248H SER 2.9 12.1 + - - +
249H ASP* 3.5 12.3 - - - +
250H VAL 3.2 0.2 - - - -
251H HIS* 1.3 74.7 - - - +
253H VAL* 1.3 64.1 + - - +
255H LYS* 3.3 16.4 + - - +
256H VAL* 3.1 34.9 + - - +
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Residues in contact with VAL 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H THR* 6.1 0.7 - - + -
220H VAL* 3.7 20.0 - - + -
228H LEU* 3.9 29.6 - - + +
239H VAL* 4.2 14.4 - - + -
241H ALA* 4.3 17.3 - - + -
244H ILE* 4.8 5.2 - - + -
249H ASP 3.2 15.8 + - - +
250H VAL* 3.8 6.7 - - - +
252H GLU* 1.3 74.5 - - - +
254H ARG* 1.3 62.0 + - - +
256H VAL* 3.3 7.5 + - - +
257H LEU* 3.1 24.5 + - + +
266H ILE* 4.2 20.2 - - + -
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Residues in contact with ARG 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H VAL* 3.0 19.4 + - - +
251H HIS* 3.5 15.0 - - + +
253H VAL* 1.3 76.7 - - - +
255H LYS* 1.3 56.4 + - - +
257H LEU* 3.4 9.1 + - - +
258H GLY* 3.1 23.6 + - - +
262H LYS* 5.0 12.0 + - - +
264H ILE 4.0 8.9 + - - -
266H ILE* 3.7 26.4 - - + +
285H ALA 2.9 27.9 + - - -
286H SER* 4.3 1.6 - - - +
287H ASP* 2.7 41.0 + - - +
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Residues in contact with LYS 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251H HIS 3.0 17.9 + - - +
252H GLU* 3.6 17.5 - - - +
254H ARG* 1.3 72.8 - - - +
256H VAL* 1.3 66.2 + - + +
258H GLY* 3.2 15.2 + - - +
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Residues in contact with VAL 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H VAL* 4.3 11.4 - - + -
225H ILE* 4.0 41.7 - - + +
228H LEU* 3.7 32.3 - - + -
229H LYS* 4.1 24.3 + - + +
232H VAL* 5.1 1.9 - - - +
252H GLU* 3.1 23.3 + - - +
253H VAL 3.3 7.6 + - - +
255H LYS* 1.3 73.8 - - + +
257H LEU* 1.3 66.0 + - - +
258H GLY* 3.5 0.5 + - - -
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Residues in contact with LEU 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H LEU* 4.1 28.0 - - + +
232H VAL* 3.9 28.1 - - + +
236H VAL* 5.9 0.4 - - + -
239H VAL* 4.3 6.3 - - + -
253H VAL* 3.1 14.8 + - + +
254H ARG* 3.5 10.8 - - - +
255H LYS 3.3 0.2 - - - -
256H VAL* 1.3 78.3 - - - +
258H GLY* 1.3 62.9 + - - +
259H GLU 3.9 0.3 + - - -
260H LYS* 4.0 4.5 + - - +
261H GLY* 3.3 36.9 + - - +
264H ILE* 3.9 28.3 - - + +
266H ILE* 3.9 32.1 - - + -
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Residues in contact with GLY 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254H ARG 3.1 14.3 + - - +
255H LYS* 3.2 14.5 + - - -
256H VAL 4.4 0.4 - - - -
257H LEU* 1.3 75.7 - - - +
259H GLU* 1.3 63.3 + - - -
261H GLY 3.8 0.2 - - - -
262H LYS* 3.3 22.5 + - - +
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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