Contacts of the helix formed by residues 252 - 263 (chain C) in PDB entry 3GXM
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 THR 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240C LEU* 3.9 27.8 - - + +
251C PHE* 1.3 77.0 - - - +
253C PRO* 1.4 78.2 - - + +
254C GLU* 3.5 13.7 + - - +
255C HIS* 2.9 21.9 + - - +
256C GLN* 2.9 18.9 + - - +
291C TRP* 4.0 0.9 - - - -
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Residues in contact with PRO 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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240C LEU* 5.9 1.3 - - + -
252C THR* 1.4 89.2 - - + +
254C GLU* 1.3 64.0 + - - +
256C GLN* 3.3 1.7 + - - +
257C ARG* 2.9 30.1 + - - +
290C HIS* 4.1 20.0 - - + +
291C TRP* 3.7 54.9 - - + +
294C VAL* 3.6 22.0 - - + -
295C VAL* 3.8 3.6 - - - +
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Residues in contact with GLU 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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252C THR* 3.5 13.0 + - - +
253C PRO* 1.3 89.9 - - - +
255C HIS* 1.3 57.4 + - - +
257C ARG* 3.4 20.8 + - - +
258C ASP* 2.9 35.9 + - - +
290C HIS* 4.5 4.9 + - - -
294C VAL* 3.6 22.0 - - + +
503C SO4 3.3 31.3 + - - +
441D LYS* 4.6 13.0 + - - -
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Residues in contact with HIS 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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196C SER* 4.2 23.3 + - - -
197C LEU 4.4 9.9 - - - -
199C GLY 5.3 4.3 - - - -
201C PRO* 4.0 15.5 - - + +
206C HIS* 2.9 35.7 + + - -
250C GLY 4.2 5.9 + - - -
251C PHE* 3.8 22.3 - + - -
252C THR* 2.9 27.1 + - - +
254C GLU* 1.3 76.3 - - - +
256C GLN* 1.3 66.3 + - - +
257C ARG 3.2 0.2 - - - -
258C ASP* 3.3 3.0 + - - -
259C PHE* 2.8 22.2 + - - +
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Residues in contact with GLN 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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232C ALA* 3.5 25.1 - - + +
233C GLU* 4.3 8.9 - - - +
236C PRO* 4.0 15.6 - - - +
251C PHE* 3.9 16.5 - - + +
252C THR 2.9 11.0 + - - +
253C PRO 3.7 7.0 - - - +
255C HIS* 1.3 76.9 - - - +
257C ARG* 1.3 55.4 + - - +
259C PHE* 3.1 3.8 + - + +
260C ILE* 2.8 56.0 + - + +
280C MET* 3.8 6.5 - - - +
281C LEU 3.1 23.3 + - - +
291C TRP* 2.9 33.6 - - + -
295C VAL* 4.3 3.4 - - + -
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Residues in contact with ARG 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 PRO 2.9 18.6 + - - +
254C GLU* 3.4 24.9 + - - +
256C GLN* 1.3 76.5 - - - +
258C ASP* 1.3 89.5 + - - +
260C ILE* 3.4 2.3 + - - +
261C ALA* 2.8 30.8 + - - +
294C VAL* 3.6 27.1 + - - +
295C VAL* 3.8 18.6 - - + +
298C ASP* 3.3 29.0 + - + +
301C ALA* 3.7 15.6 - - + +
503C SO4 2.6 45.0 + - - -
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Residues in contact with ASP 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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201C PRO* 3.4 26.4 - - + +
254C GLU* 2.9 18.7 + - - +
255C HIS* 4.0 2.1 - - - +
256C GLN 3.3 0.2 - - - -
257C ARG* 1.3 105.3 + - - +
259C PHE* 1.3 58.0 + - - +
261C ALA* 4.1 5.9 - - - +
262C ARG* 2.7 45.9 + - + +
298C ASP* 4.6 3.8 - - - +
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Residues in contact with PHE 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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197C LEU* 4.7 1.1 - - + -
201C PRO* 4.1 2.3 - - - +
206C HIS* 3.7 38.4 - + + -
209C TRP* 3.4 32.3 - + + -
210C ALA* 4.0 7.9 - - + -
213C PHE* 4.1 7.0 - + - -
232C ALA* 4.1 15.3 - - + -
251C PHE* 3.9 24.2 - + + -
255C HIS 2.8 21.6 + - - +
256C GLN* 3.7 4.3 - - - +
258C ASP* 1.3 73.6 - - - +
260C ILE* 1.3 54.9 + - + +
263C ASP* 2.9 33.3 + - + -
264C LEU* 2.7 66.0 + - + -
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Residues in contact with ILE 260 (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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232C ALA* 4.4 13.9 - - + -
256C GLN* 2.8 48.0 + - + +
257C ARG 3.7 2.7 - - - +
259C PHE* 1.3 75.5 - - + +
261C ALA* 1.3 63.3 + - - +
264C LEU* 4.1 7.6 - - + -
265C GLY* 2.9 29.6 + - - +
266C PRO* 3.3 0.9 - - - +
278C LEU* 3.7 28.0 - - + -
280C MET* 4.4 6.7 - - + -
295C VAL* 4.1 12.1 - - + -
301C ALA* 3.9 12.1 - - + +
304C TYR* 3.8 19.2 - - + -
305C VAL* 4.0 19.1 - - + -
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Residues in contact with ALA 261 (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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257C ARG 2.8 22.7 + - - +
258C ASP* 3.6 9.0 - - - +
260C ILE* 1.3 75.2 - - - +
262C ARG* 1.3 63.2 + - + +
266C PRO* 3.2 21.7 - - - +
298C ASP* 4.7 6.1 - - - +
300C GLU* 3.8 24.6 - - + +
301C ALA* 4.0 17.5 - - + +
304C TYR* 4.0 5.4 - - - -
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Residues in contact with ARG 262 (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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200C GLN* 5.1 3.6 - - - +
201C PRO* 3.7 20.5 + - + -
202C GLY* 3.9 23.7 - - - +
207C GLN* 4.0 5.5 + - - -
258C ASP* 2.7 32.3 + - + +
261C ALA* 1.3 78.1 - - + +
263C ASP* 1.3 70.6 + - - +
266C PRO* 3.5 13.0 - - - +
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Residues in contact with ASP 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C PRO* 3.6 6.9 - - - +
202C GLY* 3.0 29.0 + - - -
206C HIS* 3.1 28.1 - - - +
207C GLN* 2.3 42.6 + - - +
210C ALA* 3.9 2.0 - - + -
259C PHE* 2.9 23.7 + - + +
261C ALA 3.6 0.2 - - - -
262C ARG* 1.3 79.5 - - - +
264C LEU* 1.3 63.9 + - - +
265C GLY 3.4 1.6 - - - -
266C PRO* 3.2 3.0 - - - +
267C THR* 2.6 32.8 + - - -
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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