Contacts of the helix formed by residues 244 - 258 (chain C) in PDB entry 4UC5
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 ASP 244 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241C PRO 5.5 0.8 - - - +
242C ASN 3.4 0.4 - - - -
243C TYR* 1.3 89.0 - - + +
245C ALA* 1.3 53.7 + - - +
246C GLU* 3.4 8.7 + - - +
247C HIS* 2.7 42.2 + - - -
248C VAL* 2.8 35.3 + - - +
286C ASP* 3.8 16.8 - - - +
290C GLN* 3.7 5.8 - - - +
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Residues in contact with ALA 245 (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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244C ASP* 1.3 74.9 - - + +
246C GLU* 1.3 56.6 + - - +
248C VAL* 3.7 2.7 - - - +
249C SER* 2.9 29.6 + - - -
286C ASP* 4.2 1.2 + - - +
290C GLN* 3.2 31.5 + - + +
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Residues in contact with GLU 246 (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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244C ASP* 3.2 11.6 + - - +
245C ALA* 1.3 75.8 - - - +
247C HIS* 1.3 64.5 + - + +
249C SER* 3.4 6.6 + - - -
250C GLU* 3.0 27.4 + - - +
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Residues in contact with HIS 247 (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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235C LEU* 4.6 2.2 - - + +
240C GLU* 3.1 37.6 + - + +
241C PRO 3.4 11.5 + - - -
242C ASN* 3.3 43.5 - - + +
244C ASP* 2.7 35.9 + - - +
246C GLU* 1.3 76.4 - - + +
248C VAL* 1.3 61.7 + - - +
250C GLU* 3.5 5.4 + - + +
251C ALA* 3.1 30.1 + - - +
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Residues in contact with VAL 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 4.2 17.7 - - + -
243C TYR 3.9 11.2 - - - +
244C ASP 2.8 18.3 + - - +
245C ALA 3.7 5.4 - - - +
247C HIS* 1.3 78.4 - - - +
249C SER* 1.3 56.8 + - - +
251C ALA* 3.9 2.2 - - - +
252C ALA* 3.0 28.1 + - - +
264C LEU* 4.4 8.1 - - + +
266C ILE* 4.0 17.5 - - + -
290C GLN* 3.6 18.2 - - - +
295C GLY* 6.3 1.1 - - - -
297C ASN* 4.2 24.5 - - + +
298C ILE* 4.4 11.0 - - + -
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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
----------------------------------------------------------
245C ALA 2.9 18.0 + - - -
246C GLU* 3.6 7.9 - - - -
248C VAL* 1.3 76.5 - - - +
250C GLU* 1.3 65.0 + - - +
252C ALA* 3.4 5.7 + - - +
253C GLU* 3.1 25.5 + - - +
256C ARG* 4.8 2.1 + - - -
297C ASN* 5.4 3.1 - - - +
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Residues in contact with GLU 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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246C GLU 3.0 16.9 + - - +
247C HIS* 3.9 6.7 - - + +
248C VAL 3.4 0.2 - - - -
249C SER* 1.3 75.3 - - - +
251C ALA* 1.3 62.9 + - - +
253C GLU* 3.3 13.9 - - - +
254C GLN* 3.1 35.5 + - - +
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Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C LEU* 3.3 31.9 - - + +
235C LEU* 4.4 9.6 - - + -
247C HIS 3.1 18.0 + - - +
248C VAL* 3.9 3.8 - - - +
250C GLU* 1.3 78.3 - - - +
252C ALA* 1.3 56.5 + - - +
254C GLN* 3.2 4.4 + - - +
255C LEU* 2.9 34.4 + - + +
264C LEU* 3.9 17.9 - - + -
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Residues in contact with ALA 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 VAL 3.0 19.0 + - - +
249C SER 3.8 4.5 - - - +
251C ALA* 1.3 72.1 - - - +
253C GLU* 1.3 66.1 + - - +
255C LEU* 3.4 13.1 + - - +
256C ARG* 3.0 41.7 + - - +
262C ASP* 3.8 4.8 - - + +
264C LEU* 4.6 1.5 - - + +
297C ASN* 3.6 34.8 - - + +
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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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249C SER* 3.1 15.2 + - - +
250C GLU* 3.3 16.5 - - - +
252C ALA* 1.3 76.2 - - - +
254C GLN* 1.3 62.8 + - + +
256C ARG* 3.2 24.1 + - - +
257C ALA* 3.0 23.4 + - + +
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Residues in contact with GLN 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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195C LEU* 3.9 19.3 - - - +
196C LYS* 4.8 6.1 + - - +
199C ILE* 3.6 25.2 - - + +
250C GLU* 3.1 25.1 + - - +
251C ALA 3.2 8.2 + - - +
253C GLU* 1.3 79.0 - - + +
255C LEU* 1.3 62.8 + - - +
257C ALA* 3.3 8.1 + - - +
258C ALA* 3.1 22.7 + - - +
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Residues in contact with LEU 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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195C LEU* 5.6 0.2 - - + -
199C ILE* 3.6 26.7 - - + -
202C ILE* 4.1 4.3 - - + -
233C VAL* 4.1 33.4 - - + -
251C ALA* 2.9 23.2 + - + +
252C ALA* 3.7 5.4 - - - +
253C GLU 3.3 0.2 - - - -
254C GLN* 1.3 77.3 - - - +
256C ARG* 1.3 60.1 + - - +
258C ALA 3.3 2.3 + - - -
259C GLY 3.2 4.2 + - - -
260C VAL* 3.0 47.9 + - + +
261C THR 3.6 21.5 - - - +
262C ASP* 3.9 14.8 - - - -
263C LYS 4.9 0.4 - - - +
264C LEU* 4.1 17.3 - - + -
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Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C SER 4.8 2.0 + - - -
252C ALA* 3.0 34.3 + - - +
253C GLU* 3.5 32.2 - - - +
255C LEU* 1.3 76.1 - - - +
257C ALA* 1.3 61.9 + - - +
259C GLY* 3.1 13.2 + - - +
260C VAL 4.2 4.7 + - - +
262C ASP* 3.0 35.6 + - + +
297C ASN* 4.1 5.9 + - - +
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Residues in contact with ALA 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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253C GLU 3.0 13.0 + - - +
254C GLN* 3.5 12.3 - - - +
255C LEU 3.2 0.2 - - - -
256C ARG* 1.3 77.5 - - - +
258C ALA* 1.3 60.7 + - - +
259C GLY* 3.2 1.1 + - - -
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Residues in contact with ALA 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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199C ILE* 3.6 32.5 - - + +
200C ASP* 6.1 0.2 - - - +
254C GLN 3.1 9.4 + - - +
255C LEU 3.9 3.1 - - - +
256C ARG 3.3 0.2 - - - -
257C ALA* 1.3 76.2 - - - +
259C GLY* 1.3 62.7 + - - +
260C VAL* 3.5 11.0 + - + +
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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