Contacts of the helix formed by residues 294 - 310 (chain C) in PDB entry 2DB3
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 GLY 294 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C ILE* 3.8 2.2 - - - -
272C GLN* 3.0 35.0 + - - +
292C GLY 3.6 0.4 - - - -
293C SER* 1.3 78.1 - - - +
295C LYS* 1.3 64.1 + - - +
296C THR 3.3 2.7 - - - -
297C ALA 3.6 1.5 + - - -
298C ALA* 3.2 9.4 + - - +
2903C ANP 3.2 31.9 + - - -
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Residues in contact with LYS 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ILE* 4.1 9.0 - - + -
287C ALA 4.7 0.9 - - - +
289C ALA* 2.6 47.1 + - + +
290C GLN 2.9 17.6 + - - -
294C GLY* 1.3 74.3 - - - +
296C THR* 1.3 66.7 + - - +
298C ALA* 3.1 20.9 + - - +
299C PHE* 3.2 15.1 - - + -
399C ASP* 5.5 3.6 - - - +
400C GLU* 5.7 1.3 - - - -
431C PHE* 3.9 22.6 - - + -
432C SER* 3.9 34.1 - - - +
433C ALA* 4.0 0.6 - - - +
2803C MG 4.6 1.8 - - - -
2903C ANP 2.9 49.4 + - - +
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Residues in contact with THR 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LYS* 1.3 77.5 - - - +
297C ALA* 1.3 57.7 + - - +
299C PHE* 3.2 23.3 + - + -
300C LEU* 3.0 47.2 + - + +
330C LEU* 6.2 0.2 - - - +
333C GLN* 5.3 4.3 + - - -
334C ILE* 4.8 12.9 - - + +
337C GLU* 4.2 20.8 - - + +
341C PHE* 5.5 1.1 - - + -
399C ASP* 4.8 2.8 + - - -
2803C MG 3.8 6.9 - - - -
2903C ANP 2.7 33.0 + - - -
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C TYR* 4.2 8.1 - - + +
272C GLN* 3.6 22.2 - - - +
276C ILE* 4.9 0.2 - - - +
294C GLY 3.6 2.0 + - - -
296C THR* 1.3 73.7 - - - +
298C ALA* 1.3 68.6 + - - +
299C PHE 3.0 3.1 + - - -
300C LEU* 4.2 2.2 - - - +
301C LEU* 3.2 40.5 + - + +
302C PRO* 3.6 0.3 - - - +
341C PHE* 3.9 32.3 - - + -
2903C ANP 4.4 3.1 + - + +
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Residues in contact with ALA 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ILE* 4.1 9.9 - - + +
272C GLN* 3.8 28.0 - - + +
275C SER* 4.2 4.3 - - - -
276C ILE* 4.0 7.2 - - - +
279C ILE* 3.6 7.4 - - - +
294C GLY 3.2 14.6 + - - +
295C LYS* 3.1 18.6 + - - +
297C ALA* 1.3 78.5 - - - +
299C PHE* 1.3 55.7 + - - +
302C PRO* 3.2 18.8 - - - +
431C PHE* 3.9 14.6 - - + -
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Residues in contact with PHE 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 3.9 9.9 - - + -
295C LYS 3.2 17.9 - - - -
296C THR* 3.2 27.3 + - + -
297C ALA 3.0 0.2 - - - -
298C ALA* 1.3 82.4 - - - +
300C LEU* 1.3 92.2 + - + +
301C LEU 3.5 0.7 - - - -
302C PRO* 3.5 1.5 - - - +
303C ILE* 3.0 35.2 + - + +
323C ILE* 3.9 21.1 - - + -
334C ILE* 4.6 4.7 - - + -
397C VAL* 4.0 28.3 - - + -
399C ASP* 4.2 25.8 - - - -
429C LEU* 4.6 2.7 - - + -
431C PHE* 3.6 35.9 - + + -
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C THR* 3.0 36.7 + - + +
297C ALA* 4.3 0.9 - - - -
299C PHE* 1.3 100.1 - - + +
301C LEU* 1.3 58.2 + - - +
303C ILE* 4.7 4.5 - - + -
304C LEU* 2.8 47.0 + - + +
323C ILE* 3.7 18.6 - - + -
334C ILE* 4.3 5.8 - - + +
337C GLU* 3.8 8.3 - - + -
338C ALA* 3.7 41.7 - - + +
341C PHE* 4.0 16.8 - - + -
371C VAL* 5.6 1.1 - - + -
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C PHE* 3.8 26.9 - - + -
252C LEU* 3.9 17.3 - - + +
256C ILE* 3.9 13.9 - - + +
260C VAL* 3.7 32.1 - - + -
265C TYR* 5.4 1.6 - - + -
272C GLN* 5.6 0.4 - - - -
276C ILE* 4.5 6.3 - - + -
297C ALA* 3.2 26.6 + - + +
300C LEU* 1.3 75.3 - - - +
302C PRO* 1.3 73.0 - - + +
304C LEU* 4.3 1.2 - - - +
305C SER* 3.0 26.3 + - - -
341C PHE* 3.6 34.8 - - + -
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Residues in contact with PRO 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU* 4.1 10.5 - - + -
276C ILE* 3.7 34.8 - - + +
279C ILE* 3.8 24.2 - - + -
280C SER* 3.8 11.4 + - - +
297C ALA 3.6 1.1 - - - +
298C ALA 3.2 28.0 - - - +
299C PHE 3.5 6.5 - - - +
301C LEU* 1.3 95.1 - - + +
303C ILE* 1.3 57.0 + - - +
305C SER* 3.5 1.8 + - - -
306C LYS* 3.0 30.1 + - - +
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Residues in contact with ILE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 4.0 7.9 - - + -
299C PHE* 3.0 25.5 + - + +
300C LEU* 3.9 4.9 - - + +
301C LEU 3.2 0.6 - - - -
302C PRO* 1.3 73.2 - - - +
304C LEU* 1.3 72.9 + - + +
305C SER 3.0 2.1 + - - -
306C LYS* 3.1 14.5 + - - +
307C LEU* 3.1 14.6 + - + +
321C VAL* 3.6 36.3 - - + -
323C ILE* 5.6 2.0 - - + -
371C VAL* 5.6 0.2 - - + -
395C PHE* 3.6 30.1 - - + -
397C VAL* 3.7 30.3 - - + -
429C LEU* 3.8 12.6 - - + -
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ILE* 4.0 13.7 - - + -
300C LEU* 2.8 35.4 + - + +
301C LEU* 4.3 1.1 - - - +
303C ILE* 1.3 77.8 - - + +
305C SER* 1.3 62.5 + - - +
307C LEU* 3.4 6.3 + - + +
308C LEU* 3.3 26.9 + - - +
338C ALA* 3.9 23.3 - - + +
341C PHE* 3.7 29.8 - - + -
342C ALA* 4.1 7.0 - - + +
347C LEU* 3.7 18.8 - - + +
349C ILE* 4.3 11.2 - - + -
371C VAL* 3.9 27.8 - - + -
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Residues in contact with SER 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ASP 3.8 6.2 + - - -
252C LEU* 3.4 18.4 - - - -
253C ARG* 3.0 30.5 + - - +
256C ILE* 4.2 12.9 - - - +
280C SER* 6.1 0.2 - - - -
301C LEU 3.0 20.1 + - - -
302C PRO* 3.6 4.5 - - - -
303C ILE 3.0 0.6 - - - -
304C LEU* 1.3 75.5 - - - +
306C LYS* 1.3 59.9 + - - +
308C LEU* 3.0 5.7 + - - +
309C GLU* 2.9 30.0 + - - +
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Residues in contact with LYS 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE 5.2 1.1 - - - +
280C SER* 3.0 38.7 + - - +
282C GLY* 5.9 1.1 - - - +
302C PRO 3.0 17.2 + - - +
303C ILE 3.1 5.1 + - - +
305C SER* 1.3 74.7 - - - +
307C LEU* 1.3 58.3 + - - +
309C GLU* 3.2 31.6 + - - +
310C ASP* 2.8 47.9 + - + +
395C PHE* 3.9 26.9 - - + -
427C GLN* 5.6 2.7 - - - +
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ILE* 3.1 15.2 + - + +
304C LEU* 3.5 13.5 - - - +
306C LYS* 1.3 77.4 - - - +
308C LEU* 1.3 62.9 + - - +
310C ASP 4.8 3.6 - - - +
311C PRO* 3.4 24.1 - - - +
320C GLN* 3.6 26.9 + - + +
321C VAL* 3.8 30.1 - - + -
346C TYR* 3.9 4.5 + - - -
347C LEU* 3.9 15.5 - - + +
370C HIS* 4.1 16.6 - - + -
371C VAL* 3.8 19.7 - - + -
394C ARG* 5.8 4.9 - - - -
395C PHE* 4.4 13.7 - - + -
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ARG* 3.7 25.8 + - + +
255C ILE* 4.0 19.1 - - + -
256C ILE* 3.9 24.2 - - + -
304C LEU 3.3 17.3 + - - +
305C SER 3.0 6.8 + - - +
307C LEU* 1.3 81.0 - - - +
309C GLU* 1.3 58.2 + - - +
311C PRO* 2.9 22.0 - - - +
345C SER* 4.4 8.7 - - - -
346C TYR* 3.8 31.6 + - + -
347C LEU* 3.7 31.9 - - + -
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Residues in contact with GLU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ASP* 4.4 15.8 - - - +
253C ARG* 3.6 29.8 + - + +
305C SER* 2.9 18.2 + - - +
306C LYS* 3.2 36.6 + - - +
308C LEU* 1.3 73.3 - - - +
310C ASP* 1.3 58.9 + - + +
311C PRO* 3.2 12.5 - - - +
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Residues in contact with ASP 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C LYS* 2.8 34.8 + - + +
307C LEU* 3.8 7.6 - - - +
309C GLU* 1.3 77.2 - - + +
311C PRO* 1.3 59.4 - - - +
312C HIS* 3.0 41.9 + - - -
394C ARG* 5.4 1.9 + - - -
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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