Contacts of the helix formed by residues 295 - 308 (chain A) in PDB entry 3DL2
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A TYR* 3.5 28.3 - - + +
266A VAL* 4.0 25.1 - - + -
269A ASN* 4.7 1.1 - - + +
293A SER 3.9 0.2 - - - -
294A GLN* 1.4 86.0 - - + +
296A VAL* 1.3 67.0 + - - +
297A GLU* 3.2 9.4 + - - +
298A ILE* 3.4 22.1 + - + -
299A MET* 3.0 28.7 + - + +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 3.6 24.7 - - + +
292A ALA* 5.1 0.2 - - - -
293A SER 3.4 15.5 - - - +
294A GLN* 2.9 26.7 + - - +
295A PRO* 1.3 71.0 - - - +
297A GLU* 1.3 78.5 + - - +
299A MET* 4.0 0.2 - - - +
300A THR* 2.7 44.7 + - - +
317A ILE* 3.7 19.5 - - + +
318A GLY* 3.9 13.2 - - - +
349A GLN* 4.3 8.5 - - + -
412A SER* 3.8 11.9 - - - +
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLN* 5.3 0.2 - - - +
295A PRO* 3.2 6.3 + - - +
296A VAL* 1.3 96.2 + - + +
298A ILE* 1.3 63.6 + - + +
300A THR* 3.8 3.3 - - - -
301A TYR* 3.1 22.2 + - - +
318A GLY* 5.2 1.4 - - - -
347A GLY 4.0 3.0 - - - +
348A GLU* 3.4 17.6 - - - +
349A GLN* 2.8 33.1 + - - +
412A SER* 4.6 5.6 + - - +
426A PHE* 3.0 34.9 - - - +
427A LEU* 4.5 8.3 - - + -
462A ILE* 3.7 26.3 - - + +
466A GLN* 4.3 2.9 + - - -
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Residues in contact with ILE 298 (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 TYR* 4.8 2.2 - - - +
266A VAL* 4.0 11.4 - - + -
270A VAL* 4.6 0.4 - - + -
295A PRO* 3.4 22.2 + - + +
297A GLU* 1.3 79.2 - - - +
299A MET* 1.3 62.3 + - - +
301A TYR* 3.2 2.8 + - - +
302A VAL* 2.9 36.4 + - + +
462A ILE* 4.2 16.2 - - + +
465A LEU* 3.2 39.3 - - + -
466A GLN* 4.0 28.3 - - + +
469A LEU* 3.7 25.8 - - + -
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Residues in contact with MET 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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266A VAL* 4.8 1.6 - - - +
269A ASN* 3.6 36.3 - - - +
270A VAL* 3.8 20.4 - - + +
273A PHE* 3.5 41.8 - - + -
291A VAL* 3.8 11.2 - - + -
293A SER* 3.7 17.9 - - - +
294A GLN 3.7 16.4 - - - +
295A PRO* 3.0 25.4 + - - +
296A VAL 4.0 0.4 - - - +
298A ILE* 1.3 82.0 - - - +
300A THR* 1.3 53.5 + - - +
302A VAL* 3.5 5.6 + - + +
303A THR* 2.8 37.7 + - - -
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 3.7 11.9 - - + +
296A VAL* 2.7 23.3 + - - +
297A GLU 3.8 3.4 - - - -
299A MET* 1.3 74.3 - - - +
301A TYR* 1.3 59.2 + - - +
303A THR* 3.2 2.4 + - - -
304A TRP* 2.9 27.9 + - - +
314A VAL* 3.7 7.5 - - + +
315A ILE* 3.6 10.5 - - - +
316A GLY* 3.3 38.6 - - - +
412A SER* 3.9 3.0 - - - +
426A PHE* 3.5 31.4 - - + -
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Residues in contact with TYR 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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297A GLU 3.1 9.8 + - - +
298A ILE 3.5 4.0 - - - +
300A THR* 1.3 75.4 - - - +
302A VAL* 1.3 66.7 + - + +
304A TRP* 3.1 6.7 + + - +
305A LYS* 2.9 68.4 + - + +
424A GLU* 3.3 37.3 + - + +
426A PHE* 3.7 27.2 - + + -
466A GLN* 3.3 44.7 - - + +
471A LEU* 3.7 18.6 - - + +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 3.9 35.2 - - + -
273A PHE* 4.2 14.6 - - + -
298A ILE* 2.9 26.2 + - + +
299A MET* 3.7 10.3 - - + +
301A TYR* 1.3 80.3 - - + +
303A THR* 1.3 58.0 + - - +
305A LYS* 3.3 1.4 + - - +
306A LEU* 2.9 53.3 + - + +
469A LEU* 5.0 0.7 - - + -
471A LEU* 3.8 29.4 - - + -
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Residues in contact with THR 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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251A PHE* 4.2 4.3 - - + -
273A PHE* 3.3 22.9 - - - -
277A VAL* 3.5 21.6 - - + +
289A LEU* 3.7 28.7 - - + -
291A VAL* 3.5 20.7 - - + +
299A MET 2.8 21.4 + - - -
300A THR 3.6 4.9 - - - -
302A VAL* 1.3 75.6 - - - +
304A TRP* 1.3 55.8 + - - +
307A SER* 2.8 35.2 + - - -
314A VAL* 4.0 5.6 - - + -
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Residues in contact with TRP 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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300A THR 2.9 13.9 + - - +
301A TYR* 3.4 15.9 - + - +
303A THR* 1.3 75.9 - - - +
305A LYS* 1.3 89.4 + - + +
307A SER* 3.3 15.0 + - - -
308A THR* 3.4 10.4 + - - -
309A PHE 3.2 22.1 + - - -
311A ALA* 3.5 20.6 - - + +
314A VAL* 3.7 15.0 - - + +
414A LEU* 4.1 17.7 - - + -
424A GLU* 3.7 26.7 - - + -
426A PHE* 3.6 31.2 - + + -
171B SER* 3.1 32.0 + - - -
173B SER* 3.4 35.6 + - - +
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Residues in contact with LYS 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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301A TYR* 2.9 57.0 + - + +
302A VAL 3.8 3.8 - - - +
304A TRP* 1.3 97.4 - - + +
306A LEU* 1.3 61.4 + - + +
308A THR* 4.0 8.7 + - - -
424A GLU* 3.3 13.0 + - - -
471A LEU* 4.1 15.0 - - + -
173B SER* 3.2 44.1 + - - -
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Residues in contact with LEU 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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273A PHE* 3.5 26.7 - - + +
274A ARG* 3.6 31.9 - - + +
277A VAL* 3.8 18.2 - - + -
278A PRO* 3.8 29.3 - - + +
302A VAL* 2.9 41.7 + - + +
305A LYS* 1.3 79.3 - - + +
307A SER* 1.3 61.0 + - - +
308A THR* 4.5 3.0 + - - -
471A LEU* 4.0 16.8 - - + +
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL* 3.8 13.2 - - - -
278A PRO* 5.0 1.8 - - - -
281A GLY* 4.9 4.4 - - - -
289A LEU* 3.5 24.2 - - - +
303A THR 2.8 22.7 + - - -
304A TRP* 3.3 6.8 + - - -
306A LEU* 1.3 78.0 - - - +
308A THR* 1.3 72.4 + - - +
309A PHE* 3.3 35.0 + - - +
314A VAL* 4.0 0.2 - - - +
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Residues in contact with THR 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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304A TRP 3.4 9.2 + - - -
305A LYS 4.0 8.5 + - - -
306A LEU 3.5 3.9 + - - -
307A SER* 1.3 80.6 + - - +
309A PHE* 1.3 63.0 + - - +
172B LYS* 3.3 33.8 + - + +
173B SER* 5.2 13.1 - - - +
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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