Contacts of the helix formed by residues 307 - 324 (chain A) in PDB entry 1X3W
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 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 5.3 7.7 + - - +
305A ASN* 2.8 28.9 + - - +
306A ASP* 1.3 76.7 - - - +
308A GLU* 1.3 71.3 + - + +
309A ILE 2.9 0.7 - - - -
310A TYR* 2.5 20.1 + - - +
311A GLN* 2.6 19.5 + - + +
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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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304A LEU* 3.4 29.4 - - + +
305A ASN* 2.9 47.2 + - - +
307A ASP* 1.3 82.1 - - + +
309A ILE* 1.3 56.2 + - - +
311A GLN* 3.8 5.8 - - - +
312A LEU* 3.0 36.6 + - + +
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Residues in contact with ILE 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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27A ILE* 5.4 0.7 - - + -
28A LEU* 3.4 28.0 - - + +
31A PHE* 3.4 54.6 - - + +
32A LYS* 5.4 0.7 - - - -
301A ARG* 4.7 15.9 - - + +
302A TYR* 6.1 1.1 - - - +
304A LEU* 4.4 23.7 - - + +
305A ASN 3.1 17.8 + - - +
306A ASP* 3.5 12.8 - - - +
307A ASP 2.7 4.0 + - - -
308A GLU* 1.3 77.3 - - - +
310A TYR* 1.3 63.6 + - - +
312A LEU* 4.0 3.1 - - - +
313A ALA* 3.2 21.7 + - - +
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Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.8 6.6 + - - +
23A TYR* 3.8 27.5 - + - -
24A LYS* 3.5 59.4 - - + +
27A ILE* 3.6 22.2 - - + -
28A LEU* 3.9 14.8 - - + -
306A ASP 4.2 5.2 - - - +
307A ASP* 2.5 13.9 + - - +
309A ILE* 1.3 73.2 - - - +
311A GLN* 1.3 72.1 + - + +
312A LEU 3.0 1.3 - - - -
313A ALA* 2.8 19.4 + - - +
314A CYS* 2.9 31.5 + - - +
269B VAL 4.3 6.4 + - - -
273B PRO* 5.4 3.6 - - - +
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Residues in contact with GLN 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 ASP* 2.6 24.2 + - + +
308A GLU* 3.8 6.5 - - - +
310A TYR* 1.3 82.5 - - + +
312A LEU* 1.3 73.0 + - - +
314A CYS* 3.4 7.3 - - - +
315A ARG* 3.4 20.6 + - - +
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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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264A ASP* 3.8 31.6 - - + +
301A ARG* 2.8 37.2 - - - +
304A LEU* 4.1 14.8 - - + -
308A GLU* 3.0 21.1 + - - +
309A ILE 4.0 1.6 - - - +
310A TYR 2.9 0.4 + - - -
311A GLN* 1.3 85.5 - - - +
313A ALA* 1.3 55.4 + - - +
314A CYS 2.8 10.7 + - - -
315A ARG* 3.1 34.6 + - - +
316A ASP* 2.8 26.9 + - - +
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Residues in contact with ALA 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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23A TYR* 5.0 2.3 + - - -
27A ILE* 3.8 25.7 - - + +
30A LYS* 6.1 2.2 - - + -
31A PHE* 3.5 28.7 - - + -
301A ARG* 3.4 0.8 - - - +
309A ILE 3.2 8.8 + - - +
310A TYR 2.8 11.1 + - - +
312A LEU* 1.3 74.6 - - - +
314A CYS* 1.3 61.2 + - - +
316A ASP* 3.3 20.8 - - - +
317A GLU* 3.3 15.1 + - - +
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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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23A TYR* 4.6 6.1 - - - -
27A ILE* 6.0 0.7 - - - -
310A TYR* 2.9 46.5 + - - +
311A GLN* 3.4 12.1 - - + +
312A LEU 2.8 1.2 + - - -
313A ALA* 1.3 76.3 - - - +
315A ARG* 1.3 63.8 + - - +
316A ASP 2.8 4.8 + - - -
317A GLU* 3.0 4.7 + - - +
318A GLN* 2.8 27.0 + - - +
270B SER* 3.7 35.4 - - - +
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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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208A ASP* 3.8 31.3 + - - -
210A ARG* 5.8 1.6 - - - +
224A PHE* 3.7 45.0 - - + -
226A ASN* 6.0 0.8 - - - +
231A TRP* 3.9 27.1 - - + +
264A ASP* 4.5 14.3 + - - +
311A GLN* 3.4 13.1 + - - +
312A LEU* 3.1 33.2 + - - +
314A CYS* 1.3 76.8 - - - +
316A ASP* 1.3 74.2 + - - +
318A GLN* 3.7 12.4 - - - +
319A GLU* 3.2 19.7 + - - +
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Residues in contact with ASP 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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31A PHE* 4.1 12.7 - - + -
210A ARG* 5.6 2.9 + - - -
297A THR* 5.6 1.2 + - - +
301A ARG* 3.4 29.5 + - - -
312A LEU 2.8 19.7 + - - +
313A ALA* 3.3 12.6 - - - +
314A CYS 2.8 1.2 + - - -
315A ARG* 1.3 79.7 - - - +
317A GLU* 1.3 60.9 + - + +
319A GLU* 2.9 12.5 + - - +
320A GLN* 2.9 30.0 + - - +
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Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 4.0 14.9 + - - +
27A ILE* 6.5 0.2 - - + -
30A LYS* 5.7 1.8 + - - -
313A ALA 3.3 9.3 + - - +
314A CYS 3.0 8.9 + - - +
316A ASP* 1.3 75.9 - - + +
318A GLN* 1.3 64.4 + - - +
319A GLU 2.9 0.2 + - - -
320A GLN* 3.1 12.3 + - - +
321A ILE* 2.9 27.4 + - - +
266B ARG* 3.2 55.6 + - - +
270B SER* 3.8 17.3 - - - +
309B VAL* 3.5 23.9 - - + +
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Residues in contact with GLN 318 (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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314A CYS 2.8 23.4 + - - +
315A ARG* 3.7 11.4 - - - +
317A GLU* 1.3 71.7 - - - +
319A GLU* 1.3 57.5 + - - +
321A ILE* 3.3 20.0 - - - +
322A GLU* 3.6 9.7 + - - +
267B GLN* 2.8 55.9 + - - +
270B SER* 3.0 17.7 + - - +
271B GLY* 3.1 13.9 - - - -
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Residues in contact with GLU 319 (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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210A ARG* 2.9 43.3 + - - -
230A ARG* 6.4 1.6 - - + -
231A TRP* 3.4 12.9 + - + +
267A VAL* 4.2 11.8 - - - +
269A VAL* 4.0 3.3 - - - +
272A ARG* 3.2 32.4 + - - +
315A ARG* 3.2 10.3 + - - +
316A ASP* 2.9 13.1 + - - +
318A GLN* 1.3 76.1 - - - +
320A GLN* 1.3 59.7 + - - +
321A ILE 2.9 1.6 - - - -
322A GLU* 2.5 31.1 + - - +
323A LEU* 2.8 22.2 + - + +
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Residues in contact with GLN 320 (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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267A VAL* 4.5 14.7 - - - +
290A LYS* 3.3 36.0 + - - +
316A ASP 2.9 13.9 + - - +
317A GLU* 3.4 26.7 - - - +
319A GLU* 1.3 76.9 + - - +
321A ILE* 1.3 55.4 + - - +
323A LEU* 3.8 19.8 - - - +
324A ILE* 3.1 32.9 + - + +
266B ARG* 4.8 11.0 - - - +
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Residues in contact with ILE 321 (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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317A GLU 2.9 11.5 + - - +
318A GLN* 3.3 19.7 - - - +
319A GLU 2.9 1.0 - - - -
320A GLN* 1.3 76.2 - - - +
322A GLU* 1.3 60.3 + - + +
324A ILE* 3.8 4.3 - - + -
325A ARG* 3.1 32.5 + - - +
263B LEU* 3.3 49.6 - - + +
266B ARG* 3.6 28.9 - - + +
267B GLN* 3.6 36.3 - - + +
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Residues in contact with GLU 322 (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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230A ARG* 3.2 39.1 - - - +
231A TRP 5.4 0.3 - - - +
272A ARG* 3.1 30.7 + - - -
318A GLN 3.7 10.5 - - - +
319A GLU* 2.5 20.5 + - - +
321A ILE* 1.3 73.6 - - - +
323A LEU* 1.3 62.7 + - - +
325A ARG* 3.8 2.5 - - - -
326A GLY* 2.9 24.3 + - - -
327A LYS* 3.8 35.4 + - + -
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Residues in contact with LEU 323 (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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267A VAL* 5.1 1.6 - - + -
268A ASP 3.9 21.5 - - - +
269A VAL* 4.6 4.5 - - - -
271A LYS* 4.2 39.1 + - + +
272A ARG* 3.6 48.0 - - + +
319A GLU* 2.8 20.8 + - + +
320A GLN* 3.8 27.8 - - - +
322A GLU* 1.3 78.1 - - - +
324A ILE* 1.3 58.4 + - - +
325A ARG 3.0 0.7 - - - -
326A GLY* 2.5 30.9 + - - -
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Residues in contact with ILE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS* 3.9 25.2 + - + +
320A GLN* 3.1 18.3 + - + +
321A ILE* 3.8 12.3 - - + +
323A LEU* 1.3 78.0 - - - +
325A ARG* 1.3 65.1 + - - +
263B LEU* 4.0 33.6 - - + +
266B ARG* 5.4 2.9 - - - +
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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
------------------------------------------------------------
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