Contacts of the helix formed by residues 246 - 258 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B ILE* 3.8 3.6 - - - +
245B ARG* 1.3 85.7 - - + +
247B ALA* 1.3 61.2 + - - +
248B SER* 3.2 24.5 - - - +
249B ASP* 2.8 42.0 + - - +
250B VAL 3.7 2.1 + - - -
274B GLU* 4.3 7.0 + - - +
278B ARG* 4.1 28.7 - - - +
281B GLU* 3.3 13.7 - - - +
282B ILE* 3.7 11.6 - - - +
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Residues in contact with ALA 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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246B LYS* 1.3 70.9 - - - +
248B SER* 1.3 56.2 + - - +
250B VAL* 2.9 30.4 + - - +
251B HIS* 3.1 31.3 + - + -
281B GLU* 2.7 48.7 + - + +
282B ILE* 3.7 5.2 - - - +
284B GLU* 4.5 2.7 - - - +
285B ALA* 4.0 3.6 - - + -
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LYS* 3.2 25.2 - - - +
247B ALA* 1.3 76.4 - - - +
249B ASP* 1.3 72.2 + - - +
250B VAL 3.5 0.2 - - - -
251B HIS* 3.7 14.2 + - - +
252B GLU* 3.4 19.4 + - - +
281B GLU* 4.6 0.4 + - - -
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Residues in contact with ASP 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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219B ALA* 3.2 30.2 - - + +
220B VAL* 4.3 1.2 - - - +
243B PHE 4.6 0.3 - - - +
244B ILE* 3.7 20.3 - - + -
245B ARG* 3.5 22.5 + - - +
246B LYS* 2.8 31.3 + - - +
248B SER* 1.3 89.7 + - - +
250B VAL* 1.3 62.3 + - - +
251B HIS 3.3 0.4 - - - -
252B GLU* 3.3 7.4 + - - +
253B VAL* 3.3 27.4 + - - +
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 3.7 22.0 - - + -
246B LYS 4.2 2.7 - - - +
247B ALA* 2.9 14.3 + - - +
249B ASP* 1.3 75.0 - - - +
251B HIS* 1.3 59.0 + - + +
253B VAL* 3.5 6.7 + - - +
254B ARG* 3.0 27.9 + - - +
266B ILE* 4.1 17.5 - - + +
268B SER* 3.5 21.1 - - - +
282B ILE* 4.1 9.9 - - + +
285B ALA* 3.5 26.0 - - + +
286B SER* 3.4 22.9 - - - +
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Residues in contact with HIS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA* 3.1 35.1 + - + -
248B SER* 3.7 12.4 - - - +
250B VAL* 1.3 77.7 - - - +
252B GLU* 1.3 51.7 + - - +
254B ARG* 3.3 11.0 - - + +
255B LYS* 2.8 34.4 + - - +
284B GLU* 4.9 4.0 + - - -
285B ALA* 4.0 20.2 - - + +
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Residues in contact with GLU 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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220B VAL* 3.7 25.3 - - + +
225B ILE* 5.3 4.9 - - - +
248B SER 3.4 12.2 + - - +
249B ASP* 3.3 12.5 + - - +
250B VAL 3.2 1.0 - - - -
251B HIS* 1.3 76.5 - - - +
253B VAL* 1.3 60.6 + - - +
255B LYS* 3.1 19.9 + - - +
256B VAL* 2.9 52.9 + - + +
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Residues in contact with VAL 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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113B THR* 6.0 1.1 - - + -
220B VAL* 3.7 19.1 - - + -
228B LEU* 3.9 31.2 - - + -
239B VAL* 4.4 9.9 - - + -
241B ALA* 4.4 18.6 - - + -
244B ILE* 4.4 4.7 - - + -
249B ASP 3.3 15.2 + - - +
250B VAL* 3.8 6.5 - - - +
252B GLU* 1.3 74.9 - - - +
254B ARG* 1.3 61.6 + - - +
256B VAL* 3.4 9.3 + - - +
257B LEU* 3.1 30.8 + - + +
266B ILE* 4.1 23.8 - - + -
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Residues in contact with ARG 254 (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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250B VAL* 3.0 15.7 + - - +
251B HIS* 3.3 17.6 - - + +
252B GLU 3.2 0.2 - - - -
253B VAL* 1.3 77.4 - - - +
255B LYS* 1.3 60.3 + - - +
257B LEU* 3.5 8.1 + - - +
258B GLY* 3.1 19.8 + - - +
262B LYS* 4.9 14.6 + - - +
264B ILE 3.8 12.3 + - - -
266B ILE* 3.5 27.2 - - + +
285B ALA 3.3 24.4 + - - -
286B SER* 4.3 1.4 - - - +
287B ASP* 3.0 40.6 + - - +
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Residues in contact with LYS 255 (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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251B HIS 2.8 19.1 + - - +
252B GLU* 3.1 22.3 + - - +
254B ARG* 1.3 70.3 - - - +
256B VAL* 1.3 66.9 + - + +
258B GLY* 3.2 15.3 + - - -
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Residues in contact with VAL 256 (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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220B VAL* 4.4 9.0 - - + -
225B ILE* 4.2 38.4 - - + +
228B LEU* 4.0 29.3 - - + -
229B LYS* 4.9 17.8 + - + +
232B VAL* 5.4 1.6 - - - +
252B GLU* 2.9 38.3 + - - +
253B VAL 3.7 6.5 - - - +
254B ARG 3.4 0.2 - - - -
255B LYS* 1.3 76.7 - - + +
257B LEU* 1.3 60.2 + - - +
258B GLY* 3.5 0.9 + - - -
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Residues in contact with LEU 257 (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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228B LEU* 4.2 27.6 - - + +
231B GLY 6.0 0.2 - - - -
232B VAL* 3.8 29.5 - - + +
236B VAL* 6.3 0.2 - - + -
239B VAL* 4.6 7.0 - - + -
253B VAL* 3.1 24.8 + - + +
254B ARG* 3.8 7.9 - - - +
255B LYS 3.3 0.2 - - - -
256B VAL* 1.3 75.0 - - - +
258B GLY* 1.3 66.1 + - - +
259B GLU 3.8 0.3 + - - -
260B LYS* 3.9 4.5 + - - +
261B GLY* 3.2 37.0 + - - +
264B ILE* 4.3 22.4 - - + +
266B ILE* 3.8 31.2 - - + -
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Residues in contact with GLY 258 (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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254B ARG 3.1 13.9 + - - +
255B LYS* 3.2 13.8 + - - -
256B VAL 4.5 0.4 - - - -
257B LEU* 1.3 81.8 - - - +
259B GLU* 1.3 61.2 + - - -
261B GLY 3.7 0.5 - - - -
262B LYS* 3.3 21.0 + - - +
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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