Contacts of the helix formed by residues 246 - 258 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244G ILE* 3.5 10.2 - - - +
245G ARG* 1.3 85.0 - - + +
247G ALA* 1.3 66.2 + - - +
248G SER* 3.2 28.0 + - - +
249G ASP* 3.4 30.2 + - - +
250G VAL* 3.7 1.7 - - - +
274G GLU* 4.3 7.0 + - - +
278G ARG* 3.8 31.9 - - - +
281G GLU* 3.3 15.0 - - - +
282G ILE* 3.8 9.0 - - - -
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Residues in contact with ALA 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246G LYS* 1.3 74.9 - - - +
248G SER* 1.3 60.8 + - - +
250G VAL* 3.0 27.3 + - - +
251G HIS* 3.0 23.0 + - + +
281G GLU* 2.9 43.3 + - + +
282G ILE* 4.2 1.1 - - - +
284G GLU* 4.7 3.1 - - - +
285G ALA* 4.4 8.3 - - + -
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Residues in contact with SER 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G LYS* 3.2 33.5 + - - +
247G ALA* 1.3 76.9 - - - +
249G ASP* 1.3 59.8 + - - +
251G HIS* 3.5 8.9 + - - +
252G GLU* 3.0 29.8 + - - +
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Residues in contact with ASP 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G ALA* 3.4 29.3 + - + +
220G VAL* 4.6 1.7 - - - +
243G PHE 3.9 0.7 - - - +
244G ILE* 3.8 19.1 - - + -
245G ARG* 3.2 31.9 + - - +
246G LYS* 3.4 27.0 + - - +
247G ALA 3.1 0.4 - - - -
248G SER* 1.3 83.5 + - - +
250G VAL* 1.3 63.2 + - - +
252G GLU* 3.3 6.5 + - - +
253G VAL* 3.2 27.9 + - - +
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Residues in contact with VAL 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244G ILE* 3.7 27.6 - - + -
246G LYS 3.7 7.6 - - - +
247G ALA* 3.0 10.5 + - - +
249G ASP* 1.3 75.5 - - - +
251G HIS* 1.3 61.7 + - - +
253G VAL* 3.4 7.8 + - - +
254G ARG* 3.1 27.3 + - - +
266G ILE* 4.1 10.1 - - + +
268G SER* 3.8 5.8 - - - +
282G ILE* 4.1 8.7 - - + +
285G ALA* 3.4 26.7 - - + +
286G SER* 3.2 31.9 - - - +
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Residues in contact with HIS 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247G ALA* 3.0 26.0 + - + +
248G SER* 3.8 11.2 - - - +
249G ASP 3.3 0.2 - - - -
250G VAL* 1.3 78.1 - - - +
252G GLU* 1.3 52.0 + - - +
254G ARG* 3.2 11.3 + - + +
255G LYS* 2.7 36.0 + - - +
284G GLU* 5.5 2.2 - - - -
285G ALA* 4.3 20.5 - - + +
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Residues in contact with GLU 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G VAL* 4.3 21.3 - - + -
248G SER 3.0 18.8 + - - +
249G ASP* 3.7 7.0 - - - +
250G VAL 3.3 0.4 - - - -
251G HIS* 1.3 73.4 - - - +
253G VAL* 1.3 65.1 + - - +
255G LYS* 3.2 36.6 + - - +
256G VAL* 3.2 36.2 + - - +
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Residues in contact with VAL 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G THR* 6.1 0.7 - - + -
219G ALA 5.7 1.1 - - - +
220G VAL* 3.8 17.5 - - + -
228G LEU* 4.0 32.0 - - + +
239G VAL* 4.4 10.5 - - + -
241G ALA* 4.1 20.4 - - + -
244G ILE* 4.6 4.7 - - + -
249G ASP 3.2 16.1 + - - +
250G VAL* 3.4 7.2 + - - +
251G HIS 3.3 0.2 - - - -
252G GLU* 1.3 73.2 - - - +
254G ARG* 1.3 65.6 + - - +
256G VAL* 3.4 3.8 + - - +
257G LEU* 3.2 23.1 + - + +
266G ILE* 3.9 24.0 - - + -
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Residues in contact with ARG 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G VAL* 3.1 15.6 + - - +
251G HIS* 3.4 17.5 - - + +
253G VAL* 1.3 75.3 - - - +
255G LYS* 1.3 63.6 + - - +
257G LEU* 3.3 8.9 + - - +
258G GLY* 3.0 21.9 + - - +
262G LYS* 5.2 14.2 + - - +
264G ILE 4.2 6.6 + - - -
266G ILE* 3.6 28.6 - - - +
285G ALA 2.8 29.1 + - - -
286G SER* 3.8 10.5 - - - +
287G ASP* 2.6 36.5 + - - +
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Residues in contact with LYS 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251G HIS 2.7 20.3 + - - +
252G GLU* 3.2 35.2 + - - +
253G VAL 3.3 0.2 - - - -
254G ARG* 1.3 72.9 - - - +
256G VAL* 1.3 65.0 + - - +
258G GLY* 3.2 14.3 + - - -
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Residues in contact with VAL 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G VAL* 4.4 10.1 - - + -
225G ILE* 4.3 37.9 - - + +
228G LEU* 3.8 31.2 - - + -
229G LYS* 3.9 27.4 + - + +
232G VAL* 5.5 0.9 - - - +
252G GLU* 3.2 27.0 + - - +
253G VAL 3.7 4.9 - - - +
254G ARG 3.3 0.2 - - - -
255G LYS* 1.3 80.7 - - - +
257G LEU* 1.3 63.9 + - - +
258G GLY* 3.3 1.6 + - - -
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Residues in contact with LEU 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G LEU* 3.9 26.2 - - + +
231G GLY 6.2 0.2 - - - -
232G VAL* 3.7 31.3 - - + +
236G VAL* 6.6 0.2 - - + -
239G VAL* 4.5 12.3 - - + -
253G VAL* 3.2 18.5 + - + +
254G ARG* 3.3 10.7 + - - +
256G VAL* 1.3 76.2 - - - +
258G GLY* 1.3 65.5 + - - +
260G LYS* 4.0 5.2 + - - +
261G GLY* 3.3 37.9 + - - +
264G ILE* 4.3 14.1 - - + +
266G ILE* 3.8 30.1 - - + -
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Residues in contact with GLY 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G ARG* 3.0 14.0 + - - +
255G LYS* 3.2 14.7 + - - -
256G VAL 4.2 1.1 - - - -
257G LEU* 1.3 80.7 - - - +
259G GLU* 1.3 61.8 + - - -
261G GLY 3.8 0.5 - - - -
262G LYS* 3.5 18.7 + - - +
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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