Contacts of the helix formed by residues 279 - 295 (chain C) in PDB entry 3O9Z
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 LEU 279 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU* 3.9 22.9 - - + -
110C ILE* 3.7 27.7 - - + +
113C LEU* 3.7 21.1 - - + -
114C LYS* 3.6 45.1 - - + +
117C GLU* 3.5 33.0 - - + +
123C ARG* 5.0 4.0 - - - +
124C VAL* 3.8 13.0 + - + -
278C GLY* 1.3 71.3 - - - -
280C ASP* 1.3 64.7 + - - +
283C ALA* 3.0 29.1 + - - +
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Residues in contact with ASP 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LYS* 3.8 23.6 - - - +
123C ARG* 6.1 0.2 - - - +
278C GLY 3.3 0.8 - - - -
279C LEU* 1.3 80.9 - - - +
281C GLU* 1.3 73.1 + - - +
283C ALA* 3.9 10.6 + - - +
284C GLU* 4.9 2.3 + - - +
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Residues in contact with GLU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ARG* 5.3 2.3 + - - -
128C LEU* 5.4 0.2 - - - -
131C ARG* 3.0 45.0 + - - +
188C ASP* 3.8 1.2 - - - +
191C ALA* 5.9 1.0 - - - +
276C GLY 4.3 5.1 - - - +
277C PHE* 4.3 14.6 - - + -
278C GLY* 2.8 38.4 + - - +
280C ASP* 1.3 91.0 + - - +
282C ALA* 1.3 60.8 + - - +
283C ALA 3.6 0.2 + - - -
284C GLU* 4.5 5.9 + - - +
285C ALA 5.4 0.3 + - - -
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 3.7 31.2 - - + +
110C ILE* 5.0 0.7 - - + -
126C THR* 4.1 14.6 - - + -
128C LEU* 4.6 4.5 - - + -
188C ASP* 4.3 8.5 - - - +
278C GLY 2.9 16.4 + - - +
279C LEU 3.3 1.5 + - - +
281C GLU* 1.3 76.3 - - - +
283C ALA* 1.4 65.6 + - - +
284C GLU 3.3 1.6 + - - -
285C ALA* 3.5 6.5 + - - +
286C ILE* 3.4 24.8 + - + +
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PRO* 5.8 0.5 - - - +
110C ILE* 4.0 28.7 - - + +
114C LYS* 6.0 0.9 - - - -
279C LEU 3.0 17.8 + - - +
280C ASP* 4.2 7.6 - - - +
281C GLU 3.4 1.4 - - - -
282C ALA* 1.4 77.7 - - - +
284C GLU* 1.3 64.7 + - - +
286C ILE* 3.2 5.2 + - - +
287C ARG* 2.9 22.4 + - - +
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Residues in contact with GLU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ALA* 3.6 26.9 - - + -
195C GLY 4.2 6.7 - - - +
196C ARG* 3.8 19.2 + - - +
197C ALA* 2.8 26.9 + - - +
280C ASP 4.9 2.5 + - - +
281C GLU 4.5 4.7 + - - +
282C ALA 3.3 0.8 + - - -
283C ALA* 1.3 78.6 - - - +
285C ALA* 1.3 62.7 + - - +
287C ARG* 2.9 38.7 + - - +
288C VAL* 3.0 29.5 + - + +
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ILE* 3.6 14.6 - - + +
187C PHE* 3.7 11.9 - - + +
188C ASP* 3.4 49.5 + - + +
191C ALA* 4.5 1.8 - - + +
281C GLU 5.4 0.8 + - - -
282C ALA 3.5 4.7 + - - +
283C ALA 3.3 0.8 - - - -
284C GLU* 1.3 79.8 - - - +
286C ILE* 1.3 58.4 + - - +
288C VAL* 3.3 5.7 + - - +
289C ALA* 2.9 30.7 + - - +
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Residues in contact with ILE 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO* 4.7 2.9 - - + -
103C LEU* 3.8 18.4 - - + +
104C VAL* 3.7 40.2 - - + +
105C LEU 4.0 6.3 - - - +
106C TRP 3.9 27.8 - - - +
107C PRO* 4.1 2.7 - - + -
110C ILE* 3.9 20.2 - - + -
184C ILE* 4.2 15.9 - - + -
282C ALA* 3.4 16.5 + - + +
283C ALA* 3.2 8.4 + - - +
285C ALA* 1.3 73.5 - - - +
287C ARG* 1.3 64.1 + - - +
289C ALA* 3.9 2.3 - - - +
290C ALA* 2.9 24.6 + - - +
293C ARG* 5.1 0.2 + - - -
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Residues in contact with ARG 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PRO* 3.9 23.7 - - + +
196C ARG* 3.4 36.3 - - - +
197C ALA* 2.9 32.9 + - - +
283C ALA 2.9 12.7 + - - +
284C GLU* 2.9 45.1 + - - +
286C ILE* 1.3 76.2 - - - +
288C VAL* 1.3 65.8 + - - +
290C ALA* 3.4 2.3 + - - +
291C LEU* 3.1 53.3 + - + +
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C PHE* 4.0 28.3 - - + +
191C ALA* 6.2 0.7 - - + -
197C ALA* 3.7 16.4 - - + -
200C VAL* 4.6 7.4 - - + -
214C LEU* 4.3 16.2 - - + -
284C GLU* 3.0 35.4 + - + +
285C ALA* 3.7 7.9 - - - +
287C ARG* 1.3 77.6 - - - +
289C ALA* 1.3 66.2 + - - +
291C LEU* 3.2 11.1 + - + +
292C LEU* 3.0 31.9 + - + +
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Residues in contact with ALA 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ALA* 4.3 7.8 - - - +
180C THR* 3.5 29.1 + - + +
184C ILE* 4.1 16.4 - - + -
187C PHE* 4.9 4.2 - - + -
285C ALA 2.9 18.3 + - - +
286C ILE* 3.9 3.8 - - - +
288C VAL* 1.3 77.0 - - - +
290C ALA* 1.3 63.2 + - - +
292C LEU* 3.3 20.3 + - - +
293C ARG* 3.4 17.6 + - - +
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU 4.0 1.3 - - - +
106C TRP* 3.9 13.3 - - + -
107C PRO* 3.7 23.8 - - + -
286C ILE 2.9 19.2 + - - +
287C ARG 3.7 3.6 - - - +
288C VAL 3.2 0.2 - - - -
289C ALA* 1.3 72.5 - - - +
291C LEU* 1.3 66.6 + - - +
293C ARG* 3.1 44.5 + - - +
294C THR* 4.0 5.2 + - - +
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C VAL* 4.4 25.6 - - + -
287C ARG* 3.1 48.8 + - + +
288C VAL* 3.4 10.3 - - - +
290C ALA* 1.3 76.1 - - - +
292C LEU* 1.3 65.5 + - + +
293C ARG 3.2 0.7 + - - -
294C THR* 3.3 8.1 + - - -
295C LEU* 3.2 26.0 + - + +
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ALA* 4.4 13.5 - - + -
187C PHE* 3.4 40.8 - - + -
200C VAL* 3.6 26.9 - - + -
201C GLU 4.5 0.7 - - - +
202C VAL* 4.1 25.4 - - + -
205C ARG* 2.6 34.4 + - - -
210C ASN* 6.0 0.4 - - - +
223C TRP* 4.1 16.6 - - + +
288C VAL* 3.0 21.7 + - + +
289C ALA* 3.6 9.6 - - - +
290C ALA 3.2 0.2 - - - -
291C LEU* 1.3 77.2 - - - +
293C ARG* 1.3 53.3 + - - +
294C THR 3.3 0.2 - - - -
295C LEU* 4.0 6.1 - - + -
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Residues in contact with ARG 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU* 2.9 37.0 + - - +
106C TRP* 3.3 46.3 - - + -
172C GLU* 3.9 31.4 - - - +
176C GLY* 2.9 34.2 + - - +
180C THR* 2.8 32.9 + - - +
205C ARG* 4.1 9.9 + - - +
286C ILE* 5.1 0.6 + - - +
289C ALA* 3.4 5.7 + - - +
290C ALA* 3.1 26.0 + - - +
292C LEU* 1.3 78.8 - - - +
294C THR* 1.3 66.4 + - + +
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Residues in contact with THR 294 (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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106C TRP* 5.8 5.6 - - + -
172C GLU* 5.8 0.9 - - - +
205C ARG* 5.3 0.4 - - - -
290C ALA 4.5 3.5 + - - +
291C LEU* 3.3 7.4 + - - -
292C LEU 3.3 0.2 - - - -
293C ARG* 1.3 87.3 - - + +
295C LEU* 1.3 66.8 + - - +
296C PRO* 3.3 8.5 - - - +
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C VAL* 3.5 46.4 - - + +
201C GLU* 3.9 12.1 - - - -
202C VAL* 3.5 14.3 - - + +
205C ARG* 2.7 31.6 + - - +
291C LEU* 3.2 19.0 + - + +
292C LEU* 4.3 4.3 - - + -
293C ARG 3.6 1.4 - - - -
294C THR* 1.3 76.5 - - - +
296C PRO* 1.3 89.2 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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