Contacts of the helix formed by residues 306 - 317 (chain A) in PDB entry 3NDM
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 SER 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A GLU* 2.6 39.6 + - - +
304A ASP 5.7 0.2 - - - -
305A ILE* 1.3 85.3 + - - +
307A LYS* 1.3 62.3 + - - +
308A GLU* 3.9 4.0 - - - -
309A ALA* 3.4 18.9 - - - +
310A LYS* 3.0 33.0 + - - +
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Residues in contact with LYS 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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306A SER* 1.3 73.6 - - - +
308A GLU* 1.3 78.2 + - + +
310A LYS* 3.7 6.6 + - + +
311A ASN* 2.4 48.7 + - - +
336A LEU* 5.7 1.4 - - - +
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Residues in contact with GLU 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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172A GLU* 5.0 0.9 - - - +
306A SER* 3.3 4.7 - - - -
307A LYS* 1.3 104.4 + - - +
309A ALA* 1.3 67.3 + - - +
311A ASN* 3.9 7.8 - - - +
312A LEU* 3.1 21.7 + - - +
335A HIS* 4.4 6.6 + - - -
336A LEU* 2.8 49.2 + - + +
337A PHE* 3.4 36.4 + - + +
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Residues in contact with ALA 309 (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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172A GLU* 3.6 12.8 - - - +
268A LEU* 4.1 1.7 - - + +
272A LEU* 3.8 22.2 - - + -
305A ILE* 4.9 0.7 - - + -
306A SER* 3.4 27.1 - - - +
308A GLU* 1.3 82.0 - - - +
310A LYS* 1.3 65.7 + - + +
312A LEU* 3.0 3.6 + - - +
313A ILE* 2.9 26.9 + - + +
337A PHE* 3.4 14.3 - - + -
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Residues in contact with LYS 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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299A PHE* 4.4 35.2 - - + +
304A ASP* 2.6 38.2 - - - +
305A ILE* 4.2 4.0 - - + +
306A SER 3.0 20.8 + - - +
307A LYS* 3.9 7.2 - - - +
308A GLU 3.3 0.2 - - - -
309A ALA* 1.3 77.8 - - + +
311A ASN* 1.3 66.3 + - - +
312A LEU 3.0 0.7 + - - -
313A ILE* 3.1 8.2 + - - +
314A CYS* 2.9 30.1 + - - +
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Residues in contact with ASN 311 (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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307A LYS* 2.4 45.2 + - - +
308A GLU* 4.0 9.2 - - - +
309A ALA 3.4 0.2 - - - -
310A LYS* 1.3 75.6 - - - +
312A LEU* 1.3 55.3 + - - +
314A CYS* 4.4 2.0 - - - -
315A ALA* 3.1 23.8 + - - +
335A HIS* 3.4 24.6 + - + +
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Residues in contact with LEU 312 (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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179A THR* 4.7 10.1 - - + -
268A LEU* 3.3 19.3 - - + -
308A GLU 3.1 11.2 + - - +
309A ALA 3.0 8.9 + - - +
310A LYS 3.0 1.4 + - - -
311A ASN* 1.3 74.3 - - - +
313A ILE* 1.3 58.0 + - - +
315A ALA* 2.7 32.9 + - - +
316A PHE* 3.1 46.0 + - + -
324A LEU* 4.1 11.4 - - + -
332A ILE* 5.7 0.7 - - + -
335A HIS* 3.7 11.2 + - + -
337A PHE* 3.2 39.5 - - + -
338A PHE* 4.7 10.3 - - + -
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Residues in contact with ILE 313 (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 GLY* 4.4 5.8 - - - +
268A LEU* 3.6 24.5 - - + +
269A TYR* 3.6 42.8 - - + +
272A LEU* 5.1 6.5 - - + -
273A VAL* 5.7 1.3 - - + -
297A LEU* 4.8 0.7 - - + -
299A PHE* 4.2 16.2 - - + -
309A ALA* 2.9 14.1 + - + +
310A LYS* 3.6 8.7 - - - +
312A LEU* 1.3 77.3 - - - +
314A CYS* 1.3 69.1 + - - +
315A ALA 2.7 11.3 + - - -
316A PHE* 2.8 16.6 + - - +
317A LEU* 2.9 36.3 + - + +
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Residues in contact with CYS 314 (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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297A LEU* 3.3 34.3 - - + -
299A PHE* 3.5 28.5 - - - -
310A LYS* 2.9 18.1 + - - +
311A ASN* 4.4 3.4 - - - -
313A ILE* 1.3 75.9 - - - +
315A ALA* 1.3 56.6 + - - +
317A LEU* 4.5 2.9 - - - +
318A THR* 3.1 19.1 - - - +
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Residues in contact with ALA 315 (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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311A ASN 3.1 16.6 - - - +
312A LEU* 2.7 18.1 + - - +
314A CYS* 1.3 74.6 - - - +
316A PHE* 1.3 58.2 + - - +
318A THR* 2.7 25.6 + - - -
323A ARG* 3.7 0.2 - - - -
324A LEU* 2.9 40.4 + - + -
335A HIS* 4.9 3.8 - - + -
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Residues in contact with PHE 316 (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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179A THR* 5.6 0.4 - - + -
183A VAL* 5.4 0.9 - - + -
261A TRP* 3.7 24.0 - + + +
262A TRP* 3.5 5.1 - - - -
264A VAL* 3.3 28.0 - - + -
265A GLY* 3.3 31.2 - - - +
312A LEU* 3.1 32.4 + - + -
313A ILE 2.8 7.0 + - - +
315A ALA* 1.3 75.8 - - - +
317A LEU* 1.3 54.8 + - + +
318A THR 2.7 16.1 + - - -
323A ARG* 3.1 28.7 + - + +
324A LEU* 3.3 41.5 - - + -
332A ILE* 3.5 32.5 - - + -
338A PHE* 6.4 0.4 - + - -
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Residues in contact with LEU 317 (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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262A TRP* 3.4 32.2 - - + +
265A GLY* 3.6 36.3 - - - +
266A VAL* 4.0 4.5 - - + +
269A TYR* 5.2 0.2 - - + -
277A PRO* 4.1 11.9 - - + -
278A PHE* 3.9 16.6 - - + -
293A HIS* 3.3 20.3 - - + +
294A LYS* 5.7 0.3 - - - -
297A LEU* 3.3 46.3 - - + +
313A ILE* 2.9 27.4 + - + +
314A CYS* 4.7 1.6 - - - -
316A PHE* 1.3 75.0 - - - +
318A THR* 1.3 60.0 + - - +
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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