Contacts of the helix formed by residues 288 - 302 (chain C) in PDB entry 3M13
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 PRO 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285C GLY 5.0 1.8 - - - +
286C VAL 4.6 2.5 - - - +
287C TYR* 1.3 81.4 - - + +
289C GLU* 1.3 75.8 + - + +
291C GLU* 3.4 4.9 + - + +
292C SER* 2.8 31.1 + - - +
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Residues in contact with GLU 289 (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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271C PHE* 3.9 17.4 - - + -
273C GLN* 3.0 35.7 + - - +
287C TYR* 2.9 27.1 - - - +
288C PRO* 1.3 86.2 - - + +
290C ASP* 1.3 68.4 + - - +
292C SER* 3.4 8.7 - - - -
293C ASN* 3.1 39.1 + - - +
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Residues in contact with ASP 290 (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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222C ARG* 2.6 47.6 + - - -
224C VAL* 3.8 24.0 - - + +
273C GLN* 4.1 4.5 + - - -
284C PHE* 3.7 10.3 - - + -
285C GLY* 2.7 31.0 + - - +
287C TYR* 3.3 20.7 + - - +
288C PRO 3.1 0.2 - - - -
289C GLU* 1.3 78.8 - - - +
291C GLU* 1.3 61.0 + - - +
293C ASN* 4.8 0.3 - - - +
294C LEU* 3.6 24.6 + - - +
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Residues in contact with GLU 291 (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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228C PHE* 4.8 7.2 - - + -
284C PHE* 4.5 11.0 - - + -
285C GLY* 5.6 2.2 - - - -
287C TYR 4.5 0.2 + - - -
288C PRO* 3.4 5.7 + - + +
290C ASP* 1.3 78.7 - - - +
292C SER* 1.3 68.7 + - - +
294C LEU* 3.1 7.7 + - - +
295C ARG* 2.8 66.0 + - + +
309C LEU* 4.1 21.3 - - + +
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Residues in contact with SER 292 (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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288C PRO* 2.8 25.6 + - - +
289C GLU* 3.4 9.5 - - - -
291C GLU* 1.3 79.2 - - - +
293C ASN* 1.3 74.7 + - - +
295C ARG* 3.3 8.1 + - - +
296C ALA* 3.0 23.9 + - - +
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Residues in contact with ASN 293 (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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250C ASN* 4.5 11.7 + - - -
253C TYR* 2.9 25.8 + - - +
268C TYR* 3.3 43.5 - - + -
271C PHE* 4.1 7.6 - - - -
289C GLU* 3.1 26.8 + - - +
290C ASP 4.8 1.1 - - - +
292C SER* 1.3 87.7 + - - +
294C LEU* 1.3 60.3 + - + +
296C ALA* 3.6 5.9 - - - +
297C PHE 3.6 6.9 + - - -
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Residues in contact with LEU 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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224C VAL* 4.7 6.5 - - + +
225C VAL* 4.3 2.9 - - - -
226C GLY* 3.4 36.6 - - - +
228C PHE* 3.8 16.2 - - + -
253C TYR* 4.3 1.3 - - + -
266C LEU* 3.5 30.6 - - + +
267C GLY* 3.6 27.8 - - - -
268C TYR* 3.6 18.8 - - + +
284C PHE* 4.4 7.2 - - + -
290C ASP 3.6 18.6 - - - +
291C GLU 3.1 7.4 + - - +
293C ASN* 1.3 73.9 - - + +
295C ARG* 1.3 65.8 + - - +
297C PHE 3.1 11.1 + - - -
298C LEU* 3.1 13.9 + - - +
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Residues in contact with ARG 295 (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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228C PHE* 3.7 14.9 - - + -
291C GLU* 2.8 47.8 + - + +
292C SER* 3.7 8.5 - - - +
294C LEU* 1.3 73.2 - - - +
296C ALA* 1.3 65.3 + - - +
298C LEU* 4.4 6.5 - - - -
299C GLU* 2.9 36.5 + - - +
306C ASN* 2.8 41.8 + - - +
307C GLY 2.5 31.5 + - - -
308C GLU* 4.1 2.2 - - - +
309C LEU* 3.3 23.2 - - - +
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Residues in contact with ALA 296 (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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250C ASN* 5.0 8.3 - - + +
253C TYR* 4.6 4.5 - - - +
292C SER 3.0 11.8 + - - +
293C ASN* 3.6 14.6 - - - +
294C LEU 3.3 0.2 - - - -
295C ARG* 1.3 78.0 - - - +
297C PHE* 1.3 63.1 + - - +
299C GLU* 3.4 26.0 - - - +
300C GLU* 3.4 11.8 + - - +
301C TYR* 5.1 0.4 - - - -
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Residues in contact with PHE 297 (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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92C PHE* 4.3 7.9 - + - -
244C PHE* 4.0 12.8 - + - -
246C VAL* 3.6 33.0 - - + -
248C VAL* 4.1 12.8 - - + -
253C TYR* 3.5 47.5 + + + -
266C LEU* 3.8 14.8 - - + -
293C ASN 3.6 1.6 + - - -
294C LEU 3.1 10.7 + - - +
296C ALA* 1.3 79.0 - - - +
298C LEU* 1.3 63.8 + - + +
301C TYR* 3.0 62.7 + + + -
302C MET* 3.8 30.5 - - + -
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Residues in contact with LEU 298 (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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228C PHE* 3.8 28.9 - - + -
264C LEU* 4.1 15.3 - - + -
266C LEU* 4.3 12.3 - - + -
294C LEU 3.1 15.9 + - - +
295C ARG* 3.8 5.4 - - - +
297C PHE* 1.3 76.7 - - + +
299C GLU* 1.3 67.9 + - - +
300C GLU 3.0 1.6 - - - -
302C MET* 2.8 45.7 + - + +
303C PRO* 4.5 0.7 - - - -
305C ALA* 3.5 43.7 - - + +
306C ASN* 3.7 25.4 - - + +
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Residues in contact with GLU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ARG* 2.9 28.4 + - - +
296C ALA* 3.4 17.7 - - - +
298C LEU* 1.3 73.6 - - - +
300C GLU* 1.3 70.5 + - + +
303C PRO* 4.3 15.8 - - - +
306C ASN* 3.4 22.5 + - - +
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Residues in contact with GLU 300 (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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131C THR* 3.4 17.8 + - - +
133C PRO* 6.2 0.2 - - - +
296C ALA 3.4 14.7 + - - +
298C LEU 3.0 0.8 - - - -
299C GLU* 1.3 89.4 - - + +
301C TYR* 1.3 88.4 + - + +
303C PRO* 4.6 0.6 - - - +
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Residues in contact with TYR 301 (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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92C PHE* 4.9 5.2 - - + -
129C GLY 3.5 0.2 - - - +
130C ILE* 3.4 4.3 - - - +
131C THR* 2.9 40.1 + - - -
132C VAL* 3.9 13.7 - - + -
133C PRO* 4.0 22.2 - - + +
136C TYR* 3.6 9.8 + + - -
248C VAL* 3.4 42.8 - - + +
249C PRO* 3.7 10.0 - - - +
296C ALA 5.1 0.2 - - - -
297C PHE* 3.0 55.7 + + + +
300C GLU* 1.3 102.0 - - + +
302C MET* 1.3 66.1 + - + +
303C PRO* 3.4 6.3 - - - -
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Residues in contact with MET 302 (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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92C PHE* 4.7 8.5 - - + -
129C GLY 3.3 10.5 - - - +
130C ILE* 4.2 15.3 - - + -
235C TYR* 3.2 15.5 - - + -
241C PHE* 3.7 28.5 - - + -
244C PHE* 3.6 48.9 - - + -
264C LEU* 4.4 6.5 - - - -
297C PHE* 3.8 19.9 + - + -
298C LEU* 2.8 28.6 + - + +
301C TYR* 1.3 86.7 - - - +
303C PRO* 1.4 65.1 - - - +
305C ALA* 3.0 16.7 + - + +
306C ASN 3.8 2.3 + - - -
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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