Contacts of the helix formed by residues 303 - 317 (chain A) in PDB entry 1EZW
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 ASP 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ILE* 4.3 1.3 - - - -
235A ASP 3.2 12.6 - - - +
236A LYS 3.9 14.4 - - - +
238A GLU* 3.0 29.2 + - + +
302A GLY* 1.3 75.3 - - - +
304A PRO* 1.3 77.1 - - + +
305A ASP* 3.4 11.3 + - - +
306A THR* 3.1 23.4 + - - -
307A VAL* 2.9 19.4 + - - +
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Residues in contact with PRO 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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234A ILE* 4.0 15.9 - - + -
235A ASP 3.9 8.3 - - - +
236A LYS* 4.5 5.6 - - + -
303A ASP* 1.3 90.6 - - + +
305A ASP* 1.3 57.8 + - - +
307A VAL* 4.4 0.7 - - + -
308A VAL* 2.9 36.3 + - - +
338A LEU* 3.8 27.6 - - + -
342A GLU* 3.3 44.0 - - + +
343A VAL* 4.5 1.1 - - + -
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP* 3.1 11.8 + - - +
304A PRO* 1.3 81.7 - - - +
306A THR* 1.3 63.8 + - - +
308A VAL* 3.4 5.4 + - - +
309A ASP* 3.1 35.6 + - - +
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Residues in contact with THR 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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238A GLU* 2.5 33.9 + - - +
301A ALA 3.5 23.3 - - - +
302A GLY* 4.3 0.2 - - - -
303A ASP* 3.1 9.8 + - - -
305A ASP* 1.3 74.7 - - - +
307A VAL* 1.3 67.0 + - - +
309A ASP* 3.2 9.2 + - - +
310A LYS* 3.0 40.1 + - + +
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Residues in contact with VAL 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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232A PHE* 3.7 28.5 - - + -
233A SER 4.4 2.0 - - - +
234A ILE* 3.9 18.6 - - + -
300A ILE* 4.1 19.1 - - + +
301A ALA 4.4 1.1 - - - -
302A GLY 3.8 24.0 - - - +
303A ASP 2.9 18.6 + - - +
304A PRO 3.8 3.1 - - - +
306A THR* 1.3 74.5 - - - +
308A VAL* 1.3 65.9 + - - +
310A LYS* 3.2 2.3 + - - +
311A ILE* 2.9 37.4 + - + +
343A VAL* 4.0 12.3 - - + -
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PRO 2.9 21.9 + - - +
305A ASP* 3.7 5.6 - - - +
307A VAL* 1.3 76.2 - - - +
309A ASP* 1.3 66.8 + - - +
311A ILE 3.3 1.0 + - - -
312A GLU* 2.9 42.9 + - - +
342A GLU 3.7 8.5 - - - +
343A VAL* 3.9 16.6 - - + -
346A HIS* 3.7 37.5 - - + +
347A PHE* 3.6 22.9 - - + -
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP* 3.1 27.4 + - - +
306A THR* 3.5 11.0 - - - +
308A VAL* 1.3 80.4 - - - +
310A LYS* 1.3 62.6 + - + +
312A GLU* 3.4 22.2 + - - +
313A GLU* 3.3 25.6 + - - +
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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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200A PRO* 5.0 0.9 - - - +
296A GLU* 4.2 32.9 + - - +
299A SER 4.9 3.1 + - - +
300A ILE* 4.0 31.0 - - + -
301A ALA 3.8 16.8 - - - +
306A THR* 3.0 42.8 + - + +
307A VAL 3.2 4.2 + - - +
309A ASP* 1.3 74.5 - - + +
311A ILE* 1.3 67.5 + - - +
313A GLU* 3.2 9.3 + - - +
314A LEU* 3.1 26.0 + - + +
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Residues in contact with ILE 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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6A PHE* 3.8 17.3 - - + -
232A PHE* 4.5 4.3 - - + -
300A ILE* 4.5 11.0 - - + -
307A VAL* 2.9 29.9 + - + +
310A LYS* 1.3 74.8 - - - +
312A GLU* 1.3 64.0 + - - +
314A LEU* 3.0 8.0 + - - +
315A LEU* 2.9 29.7 + - + +
322A VAL* 3.9 33.9 - - + -
343A VAL* 3.6 30.5 - - + -
347A PHE* 3.5 27.6 - - + -
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Residues in contact with GLU 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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308A VAL* 2.9 34.4 + - - +
309A ASP* 3.5 22.4 - - - +
310A LYS 3.3 0.4 - - - -
311A ILE* 1.3 77.0 - - - +
313A GLU* 1.3 63.8 + - - +
315A LEU* 3.3 6.1 + - - +
316A LYS* 2.9 43.2 + - - +
346A HIS* 6.1 0.2 - - - +
347A PHE* 3.8 20.2 - - + -
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Residues in contact with GLU 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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200A PRO* 3.7 22.6 - - + +
309A ASP 3.3 13.4 + - - +
310A LYS* 3.2 9.5 + - - +
311A ILE 3.1 1.0 - - - -
312A GLU* 1.3 75.2 - - - +
314A LEU* 1.3 65.4 + - - +
316A LYS* 2.5 40.9 + - - +
317A ALA* 3.2 21.3 + - - +
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Residues in contact with LEU 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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198A SER 3.8 13.0 - - - +
199A ASN 3.5 10.1 - - - +
200A PRO* 3.5 31.6 - - + -
203A PHE* 4.0 17.3 - - + -
228A ALA* 5.1 5.6 - - + -
230A THR* 5.0 5.6 - - + -
300A ILE* 3.2 35.0 - - + -
310A LYS* 3.1 15.8 + - + +
311A ILE* 3.0 13.1 + - + +
313A GLU* 1.3 76.2 - - - +
315A LEU* 1.3 65.8 + - + +
317A ALA* 2.9 14.2 + - - +
318A GLY 3.3 0.7 + - - -
319A VAL* 3.2 29.3 + - + +
322A VAL* 5.2 5.8 - - + -
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Residues in contact with LEU 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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4A VAL* 4.1 35.0 - - + -
311A ILE* 2.9 28.4 + - + +
312A GLU* 3.6 7.4 - - - +
314A LEU* 1.3 77.1 - - - +
316A LYS* 1.3 62.8 + - + +
318A GLY* 3.0 13.2 + - - -
319A VAL* 3.3 26.8 + - + +
320A THR* 4.8 0.7 - - - -
322A VAL* 4.3 11.0 - - + -
347A PHE* 3.6 34.3 - - + -
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Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 2.9 42.5 + - - +
313A GLU* 2.5 45.1 + - - +
314A LEU 3.2 0.2 - - - -
315A LEU* 1.3 76.3 - - - +
317A ALA* 1.3 58.5 + - - +
318A GLY* 3.2 1.9 + - - -
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Residues in contact with ALA 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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200A PRO* 3.7 32.1 - - + +
203A PHE* 3.7 15.4 - - + +
204A GLU* 4.2 14.6 - - + +
207A VAL* 3.5 21.0 - - - +
313A GLU 3.2 11.1 + - - +
314A LEU* 2.9 11.3 + - - +
316A LYS* 1.3 76.7 - - - +
318A GLY* 1.3 56.1 + - - +
319A VAL 3.6 0.7 - - - -
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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