Contacts of the helix formed by residues 318 - 331 (chain A) in PDB entry 1A9Z
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 LEU 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A MET* 4.8 8.5 - - + -
233A TYR* 4.5 10.8 - - + -
267A ASN* 4.0 34.3 - - + +
271A ASP* 4.1 15.5 - - + +
272A VAL* 4.4 18.4 - - + -
275A ALA* 3.9 23.1 - - + -
317A THR* 1.3 74.9 - - - +
319A ASP* 1.3 64.5 + - - +
321A MET* 2.9 38.4 + - + +
322A ALA* 3.0 12.0 + - + +
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA* 3.6 24.0 - - - +
278A LYS* 3.2 38.0 + - - -
279A ALA* 5.0 0.2 - - - +
317A THR* 3.3 7.6 + - - +
318A LEU* 1.3 76.8 - - - +
320A GLU* 1.3 58.7 + - + +
322A ALA* 3.2 6.7 + - - +
323A GLN* 2.7 47.7 + - - +
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A HIS* 4.1 3.8 - - + -
315A THR 3.9 2.8 - - - +
316A ARG* 2.9 24.8 - - + +
317A THR* 2.7 45.3 + - - +
319A ASP* 1.3 76.9 - - + +
321A MET* 1.3 63.6 + - - +
323A GLN* 3.7 17.7 - - - +
324A ASP* 2.9 35.9 + - - +
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Residues in contact with MET 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 3.3 36.8 - - + -
182A GLY* 3.6 4.5 - - - -
201A MET* 4.0 6.7 - - + -
233A TYR* 3.4 32.5 - - + +
234A ILE* 4.0 0.4 - - - -
235A HIS* 3.6 39.3 - - + +
238A ASP* 5.6 0.7 - - - +
263A ALA* 5.1 6.3 - - + -
314A VAL* 6.2 1.3 - - + -
316A ARG 4.2 10.3 - - - +
317A THR 3.0 28.0 + - - +
318A LEU* 2.9 18.9 + - + +
320A GLU* 1.3 79.3 - - - +
322A ALA* 1.3 60.3 + - - +
325A THR* 2.9 27.5 + - - -
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A MET* 4.1 13.2 - - + +
272A VAL 5.1 0.7 - - - +
275A ALA* 3.7 35.2 - - + +
276A PHE* 3.9 21.1 - - + +
279A ALA* 4.0 2.9 - - + -
318A LEU* 3.0 12.0 + - + +
319A ASP 3.8 4.7 - - - +
321A MET* 1.3 74.5 - - - +
323A GLN* 1.3 58.8 + - - +
325A THR* 3.2 4.4 + - - -
326A TRP* 2.9 28.9 + - - +
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Residues in contact with GLN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LYS* 5.4 4.2 - - - +
279A ALA* 3.9 22.7 - - + +
319A ASP* 2.7 37.4 + - + +
320A GLU* 3.7 21.9 - - - +
322A ALA* 1.3 72.0 - - - +
324A ASP* 1.3 65.8 + - - +
326A TRP* 3.2 3.9 + - - +
327A HIS* 2.9 30.4 + - - +
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Residues in contact with ASP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA* 3.4 38.3 - - - +
184A HIS 4.8 3.3 - - - +
185A PRO* 4.4 22.3 - - - +
187A GLY* 5.0 0.2 - - - -
235A HIS* 2.8 23.7 + - - +
316A ARG* 5.5 0.9 - - - +
320A GLU* 2.9 23.6 + - - +
321A MET 4.1 0.9 - - - +
323A GLN* 1.3 83.3 + - - +
325A THR* 1.3 62.6 + - - +
327A HIS* 3.5 8.9 + - - +
328A TRP* 3.2 17.2 + - - +
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLY* 3.4 22.1 + - - +
183A ALA* 4.6 6.3 - - - -
201A MET* 3.8 18.7 - - + +
202A PRO* 5.5 1.8 - - + -
205A ALA* 4.2 14.8 - - + -
276A PHE* 3.8 19.5 - - + -
321A MET 2.9 19.7 + - - -
322A ALA 3.5 4.7 - - - -
323A GLN 3.1 0.4 - - - -
324A ASP* 1.3 76.7 - - - +
326A TRP* 1.3 61.2 + - - +
328A TRP* 3.2 8.0 + - + +
329A GLN* 2.8 32.3 + - + +
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Residues in contact with TRP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA* 4.0 22.7 - - + -
209A VAL* 4.0 16.4 - - + -
276A PHE* 3.9 25.1 - + + -
279A ALA* 3.5 23.5 + - + -
280A CYS* 3.6 22.5 + - + +
282A LYS* 3.9 26.9 - - - -
322A ALA 2.9 16.5 + - - +
323A GLN* 3.7 6.3 - - - +
325A THR* 1.3 77.9 - - - +
327A HIS* 1.3 53.9 + - - +
329A GLN* 4.1 17.5 - - + -
330A SER* 2.6 63.1 + - - -
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Residues in contact with HIS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A HIS 5.0 0.2 + - - -
185A PRO 3.2 21.6 + - - -
186A SER 3.4 22.0 - - - -
187A GLY* 3.5 7.2 - - - -
323A GLN 2.9 17.1 + - - +
324A ASP* 3.6 10.3 + - - +
325A THR 3.2 0.2 - - - -
326A TRP* 1.3 81.1 - - - +
328A TRP* 1.3 57.7 + - - +
330A SER* 3.7 5.2 - - - -
331A ARG* 2.8 61.9 + - + +
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Residues in contact with TRP 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA* 3.9 12.3 - - + -
187A GLY* 3.5 30.5 - - - +
188A ASP 3.5 20.4 - - - -
189A MET* 3.5 11.9 - - - +
190A GLY* 3.6 28.7 - - - -
191A GLU* 3.0 26.6 + - + +
192A ASP* 4.2 3.6 - - + -
324A ASP 3.2 12.8 + - - +
325A THR* 3.2 12.1 + - + +
327A HIS* 1.3 77.6 - - - +
329A GLN* 1.3 69.1 + - + +
332A HIS* 2.9 51.1 + + - +
335A GLY* 4.1 24.5 - - - -
336A TYR* 3.5 32.8 - + - -
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ALA* 3.6 38.8 - - + +
206A GLN* 3.8 17.1 + - - +
209A VAL* 3.8 28.0 - - + +
325A THR* 2.8 18.8 + - + +
326A TRP* 3.7 12.8 - - + +
328A TRP* 1.3 87.3 - - + +
330A SER* 1.3 61.2 + - - +
332A HIS 4.6 2.3 + - - -
333A PRO* 3.1 41.5 + - - +
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A VAL* 5.0 5.6 - - - -
326A TRP* 2.6 63.0 + - - -
327A HIS* 3.6 6.8 + - - -
329A GLN* 1.3 73.1 - - - +
331A ARG* 1.3 65.4 + - - +
332A HIS 3.4 0.3 + - - -
333A PRO* 3.6 12.5 - - - +
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Residues in contact with ARG 331 (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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186A SER 3.9 8.4 + - - -
187A GLY 3.6 7.6 - - - -
188A ASP* 3.0 30.7 + - - -
327A HIS* 2.8 56.6 + - + +
330A SER* 1.3 77.7 - - - +
332A HIS* 1.3 81.5 + - + +
333A PRO* 3.4 4.7 - - - +
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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