Contacts of the helix formed by residues 246 - 258 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244F ILE* 3.6 6.5 - - - +
245F ARG* 1.3 88.9 - - - +
247F ALA* 1.3 60.7 + - - +
248F SER* 3.2 22.7 - - - +
249F ASP* 2.9 39.3 + - - +
274F GLU* 3.6 20.8 + - - -
278F ARG* 3.7 26.2 - - - +
281F GLU* 3.3 14.4 - - - +
282F ILE* 3.8 12.5 - - - +
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Residues in contact with ALA 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F LYS* 1.3 70.5 - - - +
248F SER* 1.3 59.5 + - - +
250F VAL* 3.2 14.1 + - - +
251F HIS* 2.9 38.5 + - + -
281F GLU* 2.8 52.5 + - + +
282F ILE* 3.9 3.7 - - - +
285F ALA* 4.1 7.4 - - + -
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Residues in contact with SER 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F LYS* 3.3 30.5 - - - +
247F ALA* 1.3 73.7 - - - +
249F ASP* 1.3 64.3 + - - +
251F HIS* 3.9 12.2 + - - +
252F GLU* 3.5 19.6 + - - +
281F GLU* 4.7 0.4 + - - -
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Residues in contact with ASP 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F ALA* 3.4 28.0 - - + +
220F VAL* 4.5 1.9 - - - +
243F PHE 4.2 1.0 - - - +
244F ILE* 3.6 22.3 - - + +
245F ARG* 2.7 34.8 + - - +
246F LYS* 2.9 30.7 + - - +
248F SER* 1.3 78.2 + - - +
250F VAL* 1.3 65.1 + - - +
252F GLU* 3.3 14.0 + - - +
253F VAL* 3.4 16.5 + - - +
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Residues in contact with VAL 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F ILE* 3.8 19.3 - - + -
246F LYS 4.2 2.0 - - - +
247F ALA* 3.2 10.9 + - - +
249F ASP* 1.3 76.3 - - - +
251F HIS* 1.3 58.1 + - + +
253F VAL* 3.0 11.8 + - - +
254F ARG* 2.9 34.9 + - - +
266F ILE* 4.2 15.5 - - + -
268F SER* 3.5 18.8 - - - +
282F ILE* 4.2 9.4 - - + +
285F ALA* 3.4 33.7 - - + +
286F SER* 3.6 13.9 - - - +
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Residues in contact with HIS 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F ALA* 2.9 36.0 + - + +
248F SER* 4.0 10.4 - - - +
249F ASP 3.3 0.2 - - - -
250F VAL* 1.3 77.2 - - + +
252F GLU* 1.3 53.4 + - - +
254F ARG* 3.5 13.9 - - + +
255F LYS* 2.8 34.5 + - - +
284F GLU* 5.7 1.4 + - - -
285F ALA* 4.0 20.3 - - + +
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Residues in contact with GLU 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F ALA* 6.4 0.7 - - + -
220F VAL* 3.8 27.6 - - + +
225F ILE* 5.8 2.6 - - - +
248F SER 3.5 11.8 + - - +
249F ASP* 3.3 10.5 + - - +
250F VAL 3.1 1.2 - - - -
251F HIS* 1.3 76.4 - - - +
253F VAL* 1.3 59.8 + - - +
255F LYS* 3.6 23.2 + - - +
256F VAL* 2.9 42.0 + - - +
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Residues in contact with VAL 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F THR* 5.8 1.3 - - + -
220F VAL* 3.8 19.3 - - + -
228F LEU* 3.8 31.4 - - + -
239F VAL* 4.4 11.2 - - + -
241F ALA* 4.3 21.3 - - + -
244F ILE* 4.5 6.3 - - + -
249F ASP 3.4 16.8 - - - +
250F VAL* 3.0 5.8 + - - +
252F GLU* 1.3 72.3 - - - +
254F ARG* 1.3 60.8 + - - +
256F VAL* 3.1 6.6 + - - +
257F LEU* 2.9 36.9 + - + +
266F ILE* 4.4 15.9 - - + -
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Residues in contact with ARG 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F VAL* 2.9 15.0 + - - +
251F HIS* 3.5 19.7 - - + +
253F VAL* 1.3 76.5 - - - +
255F LYS* 1.3 56.2 + - - +
257F LEU* 3.5 6.8 + - - +
258F GLY* 3.0 25.3 + - - +
262F LYS* 5.2 10.1 + - - +
264F ILE 4.6 5.1 + - - -
266F ILE* 3.6 25.9 - - + +
285F ALA 2.7 30.5 + - - -
286F SER* 4.0 6.5 - - - +
287F ASP* 2.8 35.1 + - - +
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Residues in contact with LYS 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F HIS 2.8 19.8 + - - +
252F GLU* 3.6 25.5 + - - +
253F VAL 3.2 0.2 - - - -
254F ARG* 1.3 70.7 - - - +
256F VAL* 1.3 67.3 + - + +
258F GLY* 3.1 16.0 + - - -
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Residues in contact with VAL 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F VAL* 4.0 20.4 - - + -
225F ILE* 4.1 31.0 - - + +
228F LEU* 3.7 33.7 - - + -
229F LYS* 4.6 19.9 + - + +
232F VAL* 5.4 1.2 - - - +
252F GLU* 2.9 30.6 + - - +
253F VAL 3.1 5.1 + - - +
255F LYS* 1.3 76.9 - - + +
257F LEU* 1.3 61.8 + - - +
258F GLY* 3.4 1.0 + - - -
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Residues in contact with LEU 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228F LEU* 3.9 28.7 - - + +
232F VAL* 3.9 28.7 - - + +
236F VAL* 6.1 0.2 - - + -
239F VAL* 4.2 11.4 - - + -
253F VAL* 2.9 23.8 + - + +
254F ARG* 3.7 6.7 - - - +
256F VAL* 1.3 77.5 - - - +
258F GLY* 1.3 60.1 + - - +
260F LYS* 4.0 4.2 + - - +
261F GLY* 3.0 41.4 + - - +
264F ILE* 4.1 20.2 - - + +
266F ILE* 3.8 31.0 - - + -
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Residues in contact with GLY 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254F ARG 3.0 14.4 + - - +
255F LYS* 3.1 15.0 + - - -
256F VAL 4.3 0.9 - - - -
257F LEU* 1.3 76.6 - - - +
259F GLU* 1.3 65.7 + - - -
261F GLY 3.4 0.5 - - - -
262F 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