Contacts of the helix formed by residues 306 - 317 (chain A) in PDB entry 1XZQ
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 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A LYS* 3.5 15.3 + - - -
304A PRO* 2.9 14.2 + - + +
305A LEU* 1.3 74.6 - - - +
307A GLU* 1.3 66.9 + - + +
308A GLU* 3.4 18.5 + - - +
309A ASP* 2.4 40.0 + - - +
310A ARG* 3.2 31.5 + - - +
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Residues in contact with GLU 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 ASP* 1.3 75.4 - - + +
308A GLU* 1.3 78.1 + - - +
309A ASP 2.8 3.7 + - - -
310A ARG* 3.0 15.6 + - - +
311A LYS* 3.0 48.1 + - - +
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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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219A LYS* 3.6 22.7 + - - +
282A ILE* 3.1 50.9 + - + +
306A ASP* 3.4 12.2 + - - +
307A GLU* 1.3 90.4 + - - +
309A ASP* 1.3 59.6 + - - +
311A LYS* 3.6 11.6 - - - +
312A ILE* 3.1 26.3 - - + +
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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
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219A LYS* 3.0 30.1 + - - +
297A PHE* 4.1 16.2 - - + -
299A LEU* 4.0 16.5 - - + +
304A PRO 4.4 3.6 - - - +
305A LEU* 3.6 19.7 - - + +
306A ASP* 2.4 31.7 + - - +
307A GLU 2.8 1.6 + - - -
308A GLU* 1.3 77.6 - - - +
310A ARG* 1.3 54.8 + - - +
311A LYS 2.9 4.7 - - - -
312A ILE* 2.7 32.6 + - - +
313A LEU* 2.9 15.1 + - - +
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Residues in contact with ARG 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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305A LEU* 2.8 31.9 + - + +
306A ASP* 3.2 15.8 + - - +
307A GLU* 3.0 16.8 + - - +
309A ASP* 1.3 77.6 - - - +
311A LYS* 1.3 61.0 + - - +
313A LEU* 3.7 17.6 + - + +
314A GLU* 3.6 11.6 + - - +
338A GLU* 2.8 35.6 + - - -
342A LYS* 3.0 57.1 + - + +
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Residues in contact with LYS 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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282A ILE* 3.4 35.1 - - + +
286A LEU* 4.5 24.0 - - + +
307A GLU* 3.0 34.1 + - - +
308A GLU* 3.6 13.3 - - - +
309A ASP 2.8 0.4 + - - -
310A ARG* 1.3 77.3 - - - +
312A ILE* 1.3 58.8 + - + +
314A GLU* 2.8 29.1 + - + +
315A ARG* 3.2 6.4 + - - +
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Residues in contact with ILE 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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217A VAL* 3.8 26.5 - - + -
282A ILE* 3.5 29.6 - - + -
285A THR* 5.1 0.7 - - + -
286A LEU* 5.0 8.3 - - + -
289A ILE* 3.6 28.5 - - + -
295A VAL* 5.9 0.2 - - + -
297A PHE* 4.3 17.5 - - + -
308A GLU* 3.1 23.1 - - + +
309A ASP* 2.7 11.4 + - - +
311A LYS* 1.3 73.0 - - + +
313A LEU* 1.3 56.8 + - - +
314A GLU 2.8 9.8 + - - -
315A ARG* 3.1 5.5 + - - +
316A ILE* 3.0 40.5 + - + +
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Residues in contact with LEU 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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297A PHE* 3.5 34.8 - - + -
299A LEU* 5.1 0.2 - - + -
305A LEU* 4.1 27.6 - - + -
309A ASP 2.9 15.0 + - - +
310A ARG* 3.8 23.6 - - + +
312A ILE* 1.3 76.4 - - - +
314A GLU* 1.3 56.9 + - - +
316A ILE* 4.0 2.9 - - + -
317A LYS* 3.3 13.7 + - - +
323A VAL* 4.4 4.9 - - + -
339A ILE* 4.2 24.0 - - + -
342A LYS* 4.0 11.7 - - + +
343A LEU* 2.9 48.6 - - + +
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Residues in contact with GLU 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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310A ARG 3.6 3.1 + - - +
311A LYS* 2.8 20.3 + - + +
312A ILE 2.8 2.0 - - - -
313A LEU* 1.3 80.4 - - - +
315A ARG* 1.3 58.5 + - - +
317A LYS* 3.0 59.2 + - - +
318A ASN* 4.6 1.9 - - - +
342A LYS* 3.5 36.2 - - - +
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Residues in contact with ARG 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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286A LEU* 3.9 27.3 - - + +
289A ILE* 4.1 6.7 - - + -
290A GLU* 2.9 34.1 + - - +
311A LYS 3.2 5.0 + - - +
312A ILE* 3.1 6.8 + - - +
314A GLU* 1.3 80.5 - - - +
316A ILE* 1.3 60.8 + - + +
317A LYS 3.1 0.2 - - - -
318A ASN* 3.3 17.0 + - - +
319A LYS* 3.1 39.3 - - - +
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Residues in contact with ILE 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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289A ILE* 3.7 39.0 - - + -
295A VAL* 4.0 15.5 - - + -
297A PHE* 4.3 15.0 - - + -
312A ILE* 3.0 25.2 + - + +
313A LEU* 4.0 14.1 - - + +
315A ARG* 1.3 71.0 - - - +
317A LYS* 1.3 69.0 + - - +
318A ASN 3.1 3.1 - - - -
319A LYS* 2.8 28.5 + - + +
321A TYR* 3.0 46.1 - - + -
323A VAL* 4.0 11.7 - - + -
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Residues in contact with LYS 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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313A LEU 3.3 10.6 + - - +
314A GLU* 3.0 53.7 + - - +
315A ARG 3.1 1.2 - - - -
316A ILE* 1.3 81.1 - - - +
318A ASN* 1.3 61.3 + - + +
319A LYS 4.6 0.2 - - - +
321A TYR* 4.1 15.2 + - - -
342A LYS 3.9 18.2 - - - +
343A LEU* 4.1 23.8 - - - +
344A GLY* 5.4 1.1 - - - +
348A HIS* 6.0 0.2 - - - -
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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