Contacts of the helix formed by residues 294 - 310 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A THR* 4.1 0.2 - - - -
271A ILE* 3.4 7.9 - - - +
272A GLN* 3.0 30.3 + - - -
292A GLY 3.5 2.2 + - - -
293A SER* 1.3 76.6 - - - +
295A LYS* 1.3 64.5 + - - +
296A THR 3.3 3.8 + - - -
297A ALA 3.5 1.2 + - - -
298A ALA 3.2 8.1 + - - -
2901A ANP 3.3 32.0 + - - -
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Residues in contact with LYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ILE* 4.0 7.6 - - + -
287A ALA 4.5 2.0 - - - +
289A ALA* 2.6 50.2 + - + +
290A GLN 3.1 6.1 + - - -
293A SER* 4.5 0.2 - - - +
294A GLY* 1.3 76.6 - - - +
296A THR* 1.3 61.2 + - - +
298A ALA* 3.1 20.5 - - - +
299A PHE* 3.2 16.5 - - + -
399A ASP* 5.5 5.4 - - - +
400A GLU* 5.9 0.7 - - - -
431A PHE* 4.0 23.1 - - + -
432A SER* 3.7 35.0 - - - +
433A ALA* 3.9 0.8 - - - +
2901A ANP 2.8 56.7 + - - +
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Residues in contact with THR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A LYS* 1.3 76.7 - - - +
297A ALA* 1.3 63.3 + - - +
299A PHE* 3.2 24.9 + - + -
300A LEU* 3.0 47.7 + - + +
333A GLN* 5.2 5.2 + - + +
334A ILE* 4.4 20.4 - - + +
337A GLU* 4.6 16.7 - - + +
341A PHE* 5.7 0.9 - - - -
399A ASP* 5.1 1.7 + - - +
2801A MG 4.0 5.0 - - - -
2901A ANP 2.4 35.8 + - - -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A TYR* 4.3 8.1 - - + +
272A GLN* 3.4 22.2 - - - +
276A ILE* 5.0 0.3 - - - +
294A GLY 3.5 1.6 + - - +
295A LYS 3.4 0.2 - - - -
296A THR* 1.3 77.4 - - - +
298A ALA* 1.3 66.8 + - - +
299A PHE 2.9 1.4 + - - -
300A LEU* 4.3 1.3 - - - +
301A LEU* 3.1 41.0 + - + +
302A PRO* 3.7 0.2 - - - +
341A PHE* 3.8 32.7 - - + -
2901A ANP 4.4 4.0 + - + +
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ILE* 4.2 6.1 - - + +
272A GLN* 3.8 26.6 - - + +
275A SER* 4.0 11.6 - - - -
276A ILE* 4.1 4.4 - - - +
279A ILE* 3.4 9.3 - - - +
294A GLY 3.2 14.8 + - - +
295A LYS* 3.1 19.7 - - - +
296A THR 3.1 0.2 - - - -
297A ALA* 1.3 79.0 - - - +
299A PHE* 1.3 56.3 + - - +
302A PRO* 3.4 16.9 - - - +
431A PHE* 3.9 13.9 - - + -
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ILE* 3.8 9.6 - - + -
295A LYS 3.2 24.9 + - - -
296A THR* 3.2 22.6 + - + -
297A ALA 3.0 0.4 - - - -
298A ALA* 1.3 81.8 - - - +
300A LEU* 1.3 81.4 - - + +
301A LEU 3.6 0.7 - - - -
302A PRO* 3.6 1.7 - - - +
303A ILE* 2.9 39.4 + - + +
323A ILE* 3.9 26.7 - - + -
334A ILE* 4.7 3.8 - - + -
397A VAL* 3.9 26.9 - - + -
399A ASP* 4.3 25.4 - - + -
429A LEU* 4.5 2.0 - - + -
431A PHE* 3.7 35.4 - + + -
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A THR* 3.0 37.7 + - + +
297A ALA 4.4 0.4 - - - +
299A PHE* 1.3 82.8 - - + +
301A LEU* 1.3 58.1 + - - +
303A ILE* 3.2 4.8 + - + -
304A LEU* 2.6 52.0 + - + +
323A ILE* 3.8 28.9 - - + -
334A ILE* 4.3 5.4 - - + +
337A GLU* 4.1 3.1 - - + -
338A ALA* 3.8 39.7 - - + +
341A PHE* 3.9 23.6 - - + -
371A VAL* 5.3 2.2 - - + -
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A PHE* 4.0 25.8 - - + -
252A LEU* 3.7 17.3 - - + +
256A ILE* 3.8 20.7 - - + +
260A VAL* 3.9 19.7 - - + -
265A TYR* 5.5 1.1 - - + -
272A GLN* 5.7 0.2 - - - -
276A ILE* 4.6 6.7 - - + -
297A ALA* 3.1 25.4 + - + +
300A LEU* 1.3 76.2 - - - +
302A PRO* 1.3 65.8 - - + +
304A LEU* 3.9 1.5 - - - +
305A SER* 2.9 32.2 + - - -
341A PHE* 3.5 41.3 - - + -
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Residues in contact with PRO 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A LEU* 4.0 10.3 - - + -
276A ILE* 3.8 34.5 - - + +
279A ILE* 3.7 23.8 - - + -
280A SER* 3.9 11.6 + - - +
297A ALA 3.7 1.3 - - - +
298A ALA 3.4 26.0 - - - +
299A PHE 3.6 5.8 - - - +
300A LEU 3.7 1.3 - - - -
301A LEU* 1.3 95.3 - - + +
303A ILE* 1.3 58.9 + - - +
305A SER* 3.7 1.0 - - - -
306A LYS* 3.0 31.2 + - - +
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ILE* 4.0 10.3 - - + -
299A PHE* 2.9 28.5 - - + +
300A LEU* 3.2 6.2 + - + +
302A PRO* 1.3 76.8 - - - +
304A LEU* 1.3 70.8 + - + +
306A LYS* 3.1 16.2 + - - +
307A LEU* 3.2 15.5 + - + +
321A VAL* 3.6 35.7 - - + -
323A ILE* 5.4 1.8 - - + -
371A VAL* 5.4 1.1 - - + -
395A PHE* 3.8 28.0 - - + -
397A VAL* 3.5 32.8 - - + -
429A LEU* 3.7 11.0 - - + -
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 4.2 11.2 - - + -
300A LEU* 2.6 43.9 + - + +
301A LEU* 3.9 2.9 - - - +
303A ILE* 1.3 74.6 - - + +
305A SER* 1.3 62.7 + - - +
307A LEU* 3.1 20.8 + - + +
308A LEU* 3.5 14.7 + - - +
338A ALA* 4.0 8.5 - - + +
341A PHE* 3.4 44.0 - - + +
342A ALA* 3.9 10.5 - - + +
347A LEU* 3.9 18.8 - - + +
349A ILE* 4.6 5.8 - - + -
371A VAL* 4.2 23.8 - - + -
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ASP 3.8 5.5 + - - -
252A LEU* 3.4 22.8 - - - +
253A ARG* 3.1 33.5 + - - +
256A ILE* 4.0 13.0 - - - +
280A SER* 6.1 0.2 - - - -
301A LEU 2.9 19.1 + - - -
302A PRO* 3.7 3.6 - - - -
304A LEU* 1.3 79.3 - - - +
306A LYS* 1.3 56.4 + - - +
307A LEU 3.4 0.2 + - - -
308A LEU* 3.4 2.1 + - - -
309A GLU* 3.0 30.1 + - - +
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Residues in contact with LYS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ILE* 5.2 1.6 - - + +
280A SER* 3.0 39.2 + - - +
282A GLY* 5.8 1.1 - - - +
302A PRO 3.0 17.9 + - - +
303A ILE 3.1 5.8 + - - +
305A SER* 1.3 76.5 - - - +
307A LEU* 1.3 58.5 + - - +
309A GLU* 3.5 32.8 + - - +
310A ASP* 3.1 39.9 + - + +
394A ARG* 5.8 0.9 + - - -
395A PHE* 3.9 26.7 - - + -
427A GLN* 5.7 2.9 - - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ILE* 3.2 16.1 + - + +
304A LEU* 3.1 18.7 + - + +
306A LYS* 1.3 79.6 - - - +
308A LEU* 1.3 60.9 + - - +
310A ASP 5.1 1.1 - - - -
311A PRO* 3.4 17.2 - - - +
320A GLN* 3.7 35.4 - - + +
321A VAL* 4.1 13.9 - - + -
346A TYR* 3.2 13.0 + - - -
347A LEU* 3.8 24.2 - - + +
370A HIS* 4.1 7.2 - - + -
371A VAL* 3.7 29.6 - - + -
394A ARG* 4.4 12.3 - - - +
395A PHE* 4.8 5.6 - - + -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ARG* 4.0 27.4 + - + +
255A ILE* 3.3 32.5 - - + -
256A ILE* 3.9 17.0 - - + -
304A LEU 3.5 17.4 + - - +
305A SER* 3.4 5.0 + - - +
306A LYS 3.3 0.2 - - - -
307A LEU* 1.3 75.9 - - - +
309A GLU* 1.3 60.9 + - - +
310A ASP 3.3 0.4 - - - -
311A PRO* 3.0 20.1 - - - +
345A SER* 3.8 4.7 - - - +
346A TYR* 3.4 32.4 - - + +
347A LEU* 3.3 38.1 - - + -
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ASP* 4.4 16.8 - - - +
253A ARG* 4.0 25.2 + - + +
305A SER* 3.0 20.0 + - - +
306A LYS* 3.5 34.7 + - - +
308A LEU* 1.3 78.5 - - - +
310A ASP* 1.3 61.7 + - - +
311A PRO* 3.4 3.0 - - - +
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Residues in contact with ASP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LYS* 3.1 27.6 + - + +
307A LEU* 4.0 1.3 - - - +
309A GLU* 1.3 88.6 - - - +
311A PRO* 1.3 54.3 - - - +
312A HIS* 2.8 40.2 + - - -
394A ARG* 4.6 5.4 + - - -
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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