Contacts of the helix formed by residues 247 - 259 (chain C) in PDB entry 4QGC
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 247 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245C ILE* 3.6 9.2 - - - +
246C ARG* 1.3 106.0 - - - +
248C ALA* 1.3 65.9 + - - +
249C SER* 3.3 24.7 - - - +
250C ASP* 3.2 36.5 + - - +
251C VAL* 3.6 1.6 + - - +
275C GLU* 5.0 3.3 + - - +
279C ARG* 3.7 27.8 - - - +
282C GLU* 3.5 13.7 - - - +
283C ILE* 3.8 12.7 - - - +
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LYS* 1.3 72.4 - - - +
249C SER* 1.3 58.1 + - - +
251C VAL* 3.0 20.6 + - - +
252C HIS* 3.1 24.8 + - + +
282C GLU* 2.9 50.0 + - + +
286C ALA* 4.1 11.9 - - + -
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Residues in contact with SER 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C LYS* 3.3 31.8 - - - +
248C ALA* 1.3 77.9 - - - +
250C ASP* 1.3 62.0 + - - +
252C HIS* 4.0 9.1 - - - +
253C GLU* 3.2 30.2 + - - +
282C GLU* 4.8 0.2 + - - -
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Residues in contact with ASP 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ALA* 3.3 28.8 - - + +
221C VAL* 4.7 1.4 - - - +
245C ILE* 3.8 20.0 - - + -
246C ARG* 3.0 41.1 + - - +
247C LYS* 3.2 36.0 + - - +
248C ALA 3.1 0.4 - - - -
249C SER* 1.3 79.3 + - - +
251C VAL* 1.3 61.9 + - - +
253C GLU* 3.3 7.7 + - - +
254C VAL* 3.3 24.1 + - - +
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Residues in contact with VAL 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ILE* 3.7 12.6 - - + -
247C LYS 3.7 13.7 - - - +
248C ALA* 3.0 7.6 + - - +
250C ASP* 1.3 77.5 - - - +
252C HIS* 1.3 57.8 + - + +
254C VAL* 3.1 10.7 + - - +
255C ARG* 2.9 28.6 + - - +
267C ILE* 4.0 22.5 - - + +
269C SER* 3.4 20.0 - - - +
283C ILE* 4.3 4.3 - - + -
286C ALA* 3.3 37.0 - - + +
287C SER* 3.7 11.2 - - - +
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Residues in contact with HIS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ALA* 3.1 26.9 + - + +
249C SER* 4.3 7.7 + - - +
251C VAL* 1.3 74.2 - - - +
253C GLU* 1.3 59.9 + - - +
255C ARG* 3.5 19.5 - - + +
256C LYS* 2.9 30.0 + - - +
286C ALA* 3.5 33.6 + - + +
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C PRO* 5.6 1.0 - - - +
220C ALA* 3.9 15.8 + - - +
221C VAL* 3.9 36.6 + - + +
249C SER* 3.2 19.2 + - - +
250C ASP* 3.4 13.4 - - - +
251C VAL 3.2 0.8 - - - -
252C HIS* 1.3 77.4 - - - +
254C VAL* 1.3 59.9 + - - +
256C LYS* 3.5 12.2 + - - +
257C VAL* 3.3 27.3 + - + +
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C THR* 6.3 1.3 - - + -
221C VAL* 3.7 20.9 - - + -
229C LEU* 4.0 25.4 - - + -
240C VAL* 4.5 7.2 - - + -
242C ALA* 4.3 18.2 - - + -
245C ILE* 4.8 3.8 - - + -
250C ASP 3.5 14.1 - - - +
251C VAL* 3.1 10.3 + - - +
253C GLU* 1.3 74.7 - - - +
255C ARG* 1.3 64.5 + - - +
257C VAL* 3.2 3.8 + - - +
258C LEU* 3.1 29.8 + - + +
267C ILE* 4.0 23.3 - - + -
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Residues in contact with ARG 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C VAL* 2.9 14.6 + - - +
252C HIS* 3.5 23.9 - - + +
254C VAL* 1.3 77.5 - - - +
256C LYS* 1.3 56.0 + - - +
258C LEU* 3.5 6.3 + - - +
259C GLY* 3.0 24.6 + - - +
262C GLY 6.0 0.4 - - - -
263C LYS* 4.6 17.0 + - - +
265C ILE 4.1 7.5 + - - -
267C ILE* 3.5 30.5 - - + +
286C ALA 3.4 24.7 + - - -
287C SER 4.6 0.2 - - - -
288C ASP* 3.1 37.6 + - - +
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C HIS 2.9 18.1 + - - +
253C GLU* 3.8 12.1 - - - +
254C VAL 3.2 0.2 - - - -
255C ARG* 1.3 76.4 - - - +
257C VAL* 1.3 65.4 + - + +
259C GLY* 3.2 14.1 + - - +
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Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C VAL* 4.4 10.8 - - + -
226C ILE* 4.0 43.3 - - + +
229C LEU* 3.8 32.3 - - + -
230C LYS* 4.8 5.2 + - + +
233C VAL* 5.3 1.9 - - - +
253C GLU* 3.3 14.4 - - + +
254C VAL 3.2 7.2 + - - +
256C LYS* 1.3 77.1 - - + +
258C LEU* 1.3 65.1 + - - +
259C GLY* 3.3 0.9 + - - -
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C LEU* 4.0 28.3 - - + +
233C VAL* 3.8 27.8 - - + +
240C VAL* 4.3 9.2 - - + -
254C VAL* 3.1 20.2 + - + +
255C ARG* 3.7 8.3 - - - +
257C VAL* 1.3 75.6 - - - +
259C GLY* 1.3 60.3 + - - +
261C LYS* 4.0 3.8 + - - +
262C GLY* 3.0 42.6 + - - +
265C ILE* 4.2 21.8 - - + -
267C ILE* 3.7 37.2 - - + -
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Residues in contact with GLY 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ARG 3.0 14.5 + - - +
256C LYS* 3.2 14.6 + - - -
257C VAL 3.1 2.5 - - - -
258C LEU* 1.3 81.2 - - - +
260C GLU* 1.3 62.9 + - - -
261C LYS 3.3 0.2 - - - -
262C GLY 3.5 0.7 - - - -
263C LYS* 3.1 21.2 + - - +
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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