Contacts of the helix formed by residues 294 - 310 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ILE* 4.0 2.0 - - - -
272B GLN* 2.9 30.7 + - - +
292B GLY 3.5 2.6 + - - -
293B SER* 1.3 77.1 - - - +
295B LYS* 1.3 65.4 + - - +
296B THR 3.3 3.1 + - - -
297B ALA 3.5 1.4 + - - -
298B ALA* 3.1 12.0 + - - +
2902B ANP 3.4 31.2 + - - -
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Residues in contact with LYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ILE* 4.1 7.4 - - + -
287B ALA 4.6 1.3 - - - +
289B ALA* 2.8 46.1 + - + +
290B GLN 3.2 5.3 + - - -
293B SER* 3.6 0.6 - - - +
294B GLY* 1.3 75.3 - - - +
296B THR* 1.3 62.5 + - - +
298B ALA* 3.1 22.1 + - - +
299B PHE* 3.2 15.8 - - + -
399B ASP* 5.3 3.6 - - - +
400B GLU* 5.6 1.3 - - - -
431B PHE* 3.8 21.6 - - + -
432B SER* 3.8 37.5 - - - +
433B ALA* 4.0 0.6 - - - +
2802B MG 4.5 2.0 - - - -
2902B ANP 2.8 58.8 + - - +
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LYS* 1.3 77.1 - - - +
297B ALA* 1.3 56.9 + - - +
299B PHE* 3.2 24.5 + - + -
300B LEU* 2.9 48.9 + - + +
333B GLN* 5.2 4.5 + - - -
334B ILE* 4.6 14.1 - - + +
337B GLU* 4.2 19.6 - - + +
341B PHE* 5.6 1.1 - - + -
399B ASP* 4.7 3.8 + - - -
2802B MG 3.9 6.2 - - - -
2902B ANP 2.7 33.4 + - - -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B TYR* 4.1 18.4 - - + +
272B GLN* 3.7 20.6 - - - +
276B ILE* 4.9 0.3 - - - +
294B GLY 3.5 2.2 + - - -
295B LYS 3.4 0.2 - - - -
296B THR* 1.3 74.4 - - - +
298B ALA* 1.3 67.6 + - - +
299B PHE 3.0 3.2 + - - -
300B LEU* 4.2 2.2 - - - +
301B LEU* 3.1 36.7 + - + +
302B PRO* 3.7 0.2 - - - +
341B PHE* 4.0 26.9 - - + -
2902B ANP 4.4 3.1 + - + +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ILE* 4.2 6.7 - - + -
272B GLN* 3.8 20.5 - - + +
275B SER* 4.1 14.0 - - - -
276B ILE* 4.0 6.9 - - - +
279B ILE* 3.6 7.3 - - - +
294B GLY 3.1 13.5 + - - +
295B LYS* 3.1 17.2 + - - +
297B ALA* 1.3 77.7 - - - +
299B PHE* 1.3 56.4 + - - +
302B PRO* 3.2 19.8 - - - +
431B PHE* 3.7 18.8 - - + -
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 4.0 9.4 - - + -
295B LYS 3.2 24.4 + - - -
296B THR* 3.2 23.1 + - + -
297B ALA 3.0 0.2 - - - -
298B ALA* 1.3 81.3 - - - +
300B LEU* 1.3 94.7 + - + +
301B LEU 3.5 0.2 - - - -
302B PRO* 3.4 2.0 - - - +
303B ILE* 3.2 34.6 + - + +
323B ILE* 4.0 20.9 - - + -
334B ILE* 4.6 5.8 - - + -
397B VAL* 3.9 31.9 - - + -
399B ASP* 4.1 29.4 - - + -
429B LEU* 4.8 0.4 - - + -
431B PHE* 3.5 35.0 - + + -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B THR* 2.9 38.9 + - + +
297B ALA* 3.3 1.1 + - - -
299B PHE* 1.3 84.0 - - + +
301B LEU* 1.3 65.3 + - - +
303B ILE* 3.3 5.3 + - + +
304B LEU* 3.0 41.1 + - + +
323B ILE* 3.9 28.0 - - + -
334B ILE* 4.2 5.8 - - + +
337B GLU* 3.8 8.7 - - + -
338B ALA* 3.6 42.0 - - + +
341B PHE* 4.0 15.9 - - + -
371B VAL* 5.5 1.6 - - + -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE* 3.8 26.0 - - + -
252B LEU* 4.1 16.4 - - + -
256B ILE* 4.0 13.7 - - + +
260B VAL* 3.7 27.4 - - + -
265B TYR* 5.3 1.6 - - + -
272B GLN* 5.7 0.7 - - - -
276B ILE* 4.3 8.3 - - + -
297B ALA* 3.1 24.8 + - + +
300B LEU* 1.3 76.6 - - - +
302B PRO* 1.3 71.3 - - + +
304B LEU* 4.0 1.9 - - - +
305B SER* 3.0 24.4 + - - -
341B PHE* 3.6 40.4 - - + -
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Residues in contact with PRO 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 4.0 10.8 - - + -
276B ILE* 3.7 34.3 - - + +
279B ILE* 3.8 24.9 - - + +
280B SER* 3.9 11.9 + - - +
297B ALA 3.7 0.9 - - - +
298B ALA 3.2 27.8 - - - +
299B PHE 3.4 7.2 - - - +
301B LEU* 1.3 95.2 - - + +
303B ILE* 1.3 58.2 + - - +
305B SER* 3.6 1.9 - - - -
306B LYS* 2.9 28.8 + - - +
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Residues in contact with ILE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 4.0 8.1 - - + -
299B PHE* 3.2 22.9 - - + +
300B LEU* 3.3 5.4 + - + +
301B LEU 3.2 1.0 - - - -
302B PRO* 1.3 73.8 - - - +
304B LEU* 1.3 71.0 + - + +
305B SER 3.1 1.8 - - - -
306B LYS* 3.1 7.2 + - - +
307B LEU* 3.0 23.5 + - + +
321B VAL* 3.6 35.9 - - + -
323B ILE* 5.5 1.6 - - + -
371B VAL* 5.5 0.7 - - + -
395B PHE* 3.6 31.2 - - + -
397B VAL* 3.6 30.7 - - + -
429B LEU* 3.7 14.1 - - + -
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 3.9 15.0 - - + -
300B LEU* 3.0 39.3 + - + +
301B LEU* 4.1 1.1 - - - +
303B ILE* 1.3 78.1 - - + +
305B SER* 1.3 63.0 + - - +
307B LEU* 3.4 7.0 + - + +
308B LEU* 3.3 25.6 + - - +
338B ALA* 4.1 11.4 - - + +
341B PHE* 3.8 34.1 - - + -
342B ALA* 4.4 7.0 - - + -
347B LEU* 3.6 24.0 - - + +
349B ILE* 4.4 6.3 - - + -
371B VAL* 4.1 25.1 - - + -
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ASP 4.1 3.5 + - - -
252B LEU* 3.4 18.7 - - - +
253B ARG* 2.8 33.5 + - - +
256B ILE* 4.0 13.6 - - - +
280B SER* 6.0 0.2 - - - -
301B LEU 3.0 18.7 + - - -
302B PRO 3.6 4.9 - - - -
304B LEU* 1.3 77.0 - - - +
306B LYS* 1.3 59.9 + - - +
308B LEU* 3.1 5.5 + - - +
309B GLU* 2.9 29.7 + - - +
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE 5.1 1.6 - - - +
280B SER* 3.2 39.8 + - - +
282B GLY 5.9 0.2 - - - +
302B PRO 2.9 16.9 + - - +
303B ILE 3.1 5.4 + - - +
305B SER* 1.3 77.9 - - - +
307B LEU* 1.3 55.8 + - - +
309B GLU* 2.8 30.6 + - - +
310B ASP* 2.8 40.6 + - + +
394B ARG* 3.6 14.4 + - - +
395B PHE* 3.8 25.6 - - + -
427B GLN* 5.5 2.7 - - - +
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ILE* 3.0 19.2 + - + +
304B LEU* 3.6 9.6 - - + +
306B LYS* 1.3 76.5 - - - +
308B LEU* 1.3 62.0 + - - +
311B PRO* 3.3 26.3 - - - +
320B GLN* 3.6 27.1 + - + +
321B VAL* 3.8 21.5 - - + -
347B LEU* 4.0 22.0 - - + +
370B HIS* 4.3 14.6 - - + +
371B VAL* 3.7 29.6 - - + -
394B ARG* 3.8 18.6 - - - +
395B PHE* 4.3 7.2 - - + -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ARG* 3.3 32.5 + - + +
255B ILE* 3.2 42.4 - - + -
256B ILE* 3.9 18.6 - - + -
304B LEU 3.3 14.8 + - - +
305B SER 3.1 7.2 + - - +
307B LEU* 1.3 81.6 - - - +
309B GLU* 1.3 60.6 + - - +
311B PRO* 3.5 12.0 - - - +
345B SER* 4.5 6.1 - - - -
346B TYR 5.2 2.9 - - - +
347B LEU* 3.5 36.3 - - + -
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ASP* 4.5 13.7 - - - +
253B ARG* 3.9 25.7 + - + +
305B SER* 2.9 17.7 + - - +
306B LYS* 2.8 35.5 + - - +
308B LEU* 1.3 75.0 - - - +
310B ASP* 1.3 61.3 + - + +
311B PRO* 3.1 12.6 - - - +
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Residues in contact with ASP 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LYS* 2.8 26.2 + - + +
307B LEU 3.8 3.4 - - - -
309B GLU* 1.3 78.0 - - + +
311B PRO* 1.3 58.8 - - - +
312B HIS* 2.9 32.8 + - - -
394B ARG* 2.8 32.9 + - - +
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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