Contacts of the helix formed by residues 246 - 259 (chain C) in PDB entry 1D2H
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 CYS 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C HIS* 4.5 0.7 - - - -
178C ASP* 2.7 30.7 - - - +
181C LEU* 2.7 40.8 - - - -
244C PRO* 6.0 0.2 - - - -
245C HIS* 1.3 71.0 - - - +
247C LEU* 1.3 70.3 + - - +
248C ALA* 3.0 6.5 + - + +
249C SER* 3.1 18.3 + - - +
250C PHE 3.4 7.1 + - - -
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Residues in contact with LEU 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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174C HIS* 4.1 10.2 + - + -
178C ASP* 2.7 16.4 + - - +
245C HIS 3.7 1.8 + - - -
246C CYS* 1.3 69.0 - - - +
248C ALA* 1.3 56.1 + - - +
250C PHE* 3.0 0.5 + - - -
251C THR* 2.5 64.8 + - - +
266C VAL* 4.1 11.4 - - + -
273C TYR* 3.5 21.3 - - + +
284C PHE* 3.3 43.5 - - + -
286C HIS* 3.3 25.1 - - - +
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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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178C ASP* 4.7 1.2 + - - +
246C CYS* 3.0 6.8 + - + +
247C LEU* 1.3 80.2 - - - +
249C SER* 1.3 64.0 + - - +
251C THR* 3.0 13.4 + - - -
252C GLU* 3.1 14.3 + - - +
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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
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150C GLN* 3.7 21.6 + - - -
245C HIS* 4.2 10.3 - - - -
246C CYS* 3.1 15.8 + - - +
248C ALA* 1.3 78.9 - - - +
250C PHE* 1.3 57.7 + - - +
252C GLU* 4.0 5.6 - - - +
253C LEU* 2.9 29.5 + - - +
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Residues in contact with PHE 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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140C PHE* 2.9 42.6 - + - -
157C LEU* 3.9 11.4 - - + -
172C ILE* 3.3 36.3 - - + -
173C ASP 5.1 0.7 - - - -
174C HIS* 3.6 31.0 - - + -
245C HIS* 3.9 26.9 - + + -
246C CYS 3.4 4.1 + - - +
247C LEU 3.0 3.2 + - - +
249C SER* 1.3 76.4 + - - +
251C THR* 1.3 69.6 + - - +
252C GLU 3.0 1.8 - - - -
253C LEU* 4.0 9.0 - - + -
254C VAL* 2.9 44.6 + - + +
286C HIS* 3.7 18.2 - + - -
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Residues in contact with THR 251 (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 LEU* 2.5 52.5 + - - +
248C ALA* 3.4 6.5 - - - -
250C PHE* 1.3 71.9 - - - +
252C GLU* 1.3 59.5 + - + +
254C VAL* 3.2 15.1 - - - +
255C GLN* 3.4 18.6 - - - +
264C HIS* 3.7 22.0 + - + +
266C VAL* 4.6 1.7 - - + +
286C HIS* 3.4 12.9 - - - -
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Residues in contact with GLU 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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154C ARG* 5.2 8.1 + - - -
248C ALA 3.1 12.2 + - - +
249C SER* 4.0 5.1 - - - +
250C PHE 3.0 0.2 - - - -
251C THR* 1.3 78.2 - - + +
253C LEU* 1.3 67.1 + - - +
254C VAL 3.0 3.3 + - - -
255C GLN* 3.1 22.5 + - - +
256C GLU* 3.1 14.0 + - + +
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Residues in contact with LEU 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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150C GLN* 4.3 18.6 - - + +
153C HIS* 3.8 24.2 - - + -
154C ARG* 3.2 50.3 - - + +
157C LEU* 3.8 29.6 - - + +
245C HIS* 4.5 7.9 - - - +
249C SER* 2.9 21.6 + - - +
250C PHE* 3.2 11.2 + - + +
252C GLU* 1.3 78.5 + - - +
254C VAL* 1.3 62.4 + - - +
256C GLU* 3.3 31.2 - - - +
257C ALA 3.5 2.1 + - - -
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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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157C LEU* 4.3 13.4 - - + +
170C LEU* 4.2 13.0 - - + -
172C ILE* 4.9 3.4 - - + -
250C PHE* 2.9 43.0 + - + +
251C THR 3.2 11.7 - - - +
253C LEU* 1.3 73.8 - - - +
255C GLN* 1.3 68.4 + - - +
256C GLU 3.1 1.8 - - - -
257C ALA* 2.7 36.4 + - + +
258C PHE* 3.8 3.7 + - - -
264C HIS* 4.0 10.5 - - - +
286C HIS* 3.8 17.0 - - + +
288C LEU* 3.4 23.8 - - + -
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Residues in contact with GLN 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 THR* 3.4 22.0 + - - +
252C GLU* 3.1 14.8 + - - +
254C VAL* 1.3 81.9 - - - +
256C GLU* 1.3 50.4 + - - +
258C PHE* 2.8 11.6 + - - +
259C GLY 2.7 28.4 + - - -
260C GLY* 3.6 9.8 + - - +
262C CYS* 4.1 19.5 - - - +
264C HIS* 3.5 37.8 + - + +
288C LEU* 5.2 1.1 - - + -
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Residues in contact with GLU 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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154C ARG* 2.8 59.9 + - - +
157C LEU* 5.2 0.5 - - - +
158C LYS* 4.9 5.2 - - - +
252C GLU* 3.1 10.3 + - + +
253C LEU* 3.3 23.0 - - - +
254C VAL 3.1 0.2 - - - -
255C GLN* 1.3 78.9 - - - +
257C ALA* 1.3 67.9 + - - +
258C PHE 3.7 0.2 - - - -
259C GLY* 2.8 19.8 + - - +
260C GLY 5.0 0.2 - - - +
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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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157C LEU* 3.8 27.4 - - + +
158C LYS* 4.4 16.7 - - - +
161C ALA* 3.8 26.3 - - + +
170C LEU* 5.9 0.7 - - + -
253C LEU 3.5 1.8 + - - -
254C VAL* 2.7 21.9 + - + +
256C GLU* 1.3 87.7 - - - +
258C PHE* 1.3 60.5 + - + +
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Residues in contact with PHE 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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161C ALA* 3.4 39.9 - - + -
164C VAL* 3.9 7.2 - - + -
170C LEU* 3.7 29.6 - - + -
254C VAL 3.9 12.1 - - - -
255C GLN 2.8 6.7 + - - +
256C GLU 3.7 0.2 - - - -
257C ALA* 1.3 77.1 - - + +
259C GLY* 1.3 66.6 + - - +
261C ARG* 3.3 35.5 + - - +
262C CYS* 3.9 7.9 - - + -
288C LEU* 3.5 36.3 - - + -
290C LYS* 3.5 39.9 - - + +
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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 GLN 2.7 8.5 + - - -
256C GLU* 2.8 19.0 + - - -
258C PHE* 1.3 80.2 - - - +
260C GLY* 1.3 54.8 + - - -
261C ARG* 3.1 21.8 + - - -
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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