Contacts of the helix formed by residues 306 - 321 (chain A) in PDB entry 1W31
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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305A VAL* 1.3 73.6 - - - +
307A LEU* 1.3 58.9 + - - +
308A LYS* 3.9 10.9 + - - +
309A THR* 2.7 36.7 + - - +
310A ILE* 2.8 35.9 + - - +
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Residues in contact with LEU 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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296A LEU* 4.1 32.8 - - + +
297A HIS* 3.4 42.2 - - + +
300A ALA* 4.0 13.5 - - + +
305A VAL 3.8 3.6 + - - -
306A ASP* 1.3 74.0 + - - +
308A LYS* 1.3 58.0 + - - +
310A ILE* 3.5 5.1 - - + +
311A ALA* 2.8 36.0 + - + +
330A LEU* 5.0 16.2 - - + -
333A GLU* 5.6 3.8 - - + +
337A TRP* 5.0 8.1 - - + -
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Residues in contact with LYS 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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306A ASP* 3.4 11.3 + - - +
307A LEU* 1.3 78.7 - - - +
309A THR* 1.3 64.1 + - - +
311A ALA* 3.5 0.9 - - - +
312A PHE* 3.0 52.1 + - + -
337A TRP* 3.7 51.6 + - + +
340A GLU* 3.1 27.3 + - - +
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Residues in contact with THR 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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306A ASP* 2.7 35.1 + - + +
308A LYS* 1.3 78.9 - - - +
310A ILE* 1.3 61.2 + - + +
312A PHE* 3.1 8.6 + - - +
313A GLU* 2.9 35.6 + - - +
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Residues in contact with ILE 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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296A LEU* 4.1 36.1 - - + +
305A VAL* 4.0 37.0 - - + -
306A ASP 2.8 21.0 + - - +
307A LEU* 3.5 10.1 - - + +
309A THR* 1.3 76.1 - - + +
311A ALA* 1.3 65.7 + - - +
313A GLU* 3.9 27.1 - - + +
314A SER* 3.0 28.5 + - - +
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Residues in contact with ALA 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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296A LEU* 4.3 5.2 - - + -
307A LEU* 2.8 23.2 + - + +
308A LYS 3.5 4.5 - - - +
310A ILE* 1.3 78.8 - - + +
312A PHE* 1.3 58.0 + - - +
314A SER* 2.9 18.6 + - - -
315A HIS* 3.1 22.5 + - - -
330A LEU* 3.9 22.4 - - + -
334A PHE* 3.8 4.0 - - + -
337A TRP* 3.7 22.4 - - + -
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Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.4 12.6 - - + -
308A LYS* 3.0 39.4 + - + +
309A THR* 3.4 9.4 - - - +
311A ALA* 1.3 76.9 - - - +
313A GLU* 1.3 55.6 + - - +
315A HIS* 4.2 0.4 - - - +
316A GLN* 2.7 40.5 + - + +
334A PHE* 3.7 22.0 - + - -
337A TRP* 3.4 54.3 - + + -
338A LEU* 4.5 9.6 - - + -
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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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309A THR* 2.9 24.8 + - + +
310A ILE* 3.4 24.9 + - + +
312A PHE* 1.3 76.1 - - - +
314A SER* 1.3 61.2 + - - +
316A GLN* 3.9 3.5 - - - +
317A GLY* 3.0 19.9 + - - -
320A ARG* 5.0 3.4 + - - +
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Residues in contact with SER 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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266A THR* 4.0 21.3 - - - -
269A LEU* 5.2 1.0 - - - +
288A HIS* 4.6 1.3 + - - -
296A LEU* 3.9 14.7 - - - +
310A ILE* 3.0 17.7 + - - +
311A ALA* 2.9 20.4 + - - -
313A GLU* 1.3 77.6 - - - +
315A HIS* 1.3 72.1 + - - +
317A GLY* 3.1 10.2 + - - -
318A PHE* 3.2 23.8 + - - -
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Residues in contact with HIS 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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36A LEU* 4.4 8.5 - - + -
41A LEU* 5.1 2.5 - - + -
288A HIS* 3.7 26.5 - + - -
311A ALA 3.1 18.7 + - - +
312A PHE 4.2 1.3 - - - +
314A SER* 1.3 81.5 + - - +
316A GLN* 1.4 64.4 - - - +
317A GLY 3.0 1.3 - - - -
318A PHE* 3.1 40.4 + + + +
319A LEU* 3.4 11.0 + - - +
326A ILE* 3.8 26.6 - - + +
328A THR* 3.0 27.0 + - + -
330A LEU* 4.1 9.2 - - + -
334A PHE* 3.3 30.3 - + + -
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Residues in contact with GLN 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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32A SER* 4.4 14.5 - - - -
33A GLU 5.5 0.3 + - - -
34A ARG 3.4 26.9 + - - +
35A GLN* 4.7 0.8 - - - +
36A LEU* 4.5 12.4 - - + +
312A PHE* 2.7 22.9 + - + +
313A GLU* 3.9 3.4 - - - +
315A HIS* 1.4 75.7 - - - +
317A GLY* 1.3 62.3 + - - +
319A LEU* 3.0 18.4 + - - +
320A ARG* 2.9 38.4 + - + +
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Residues in contact with GLY 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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269A LEU* 3.6 11.0 - - - +
313A GLU 3.0 12.0 + - - -
314A SER* 3.5 7.0 - - - -
315A HIS 3.0 0.4 - - - -
316A GLN* 1.3 79.0 - - - +
318A PHE* 1.3 55.9 + - - +
320A ARG* 3.5 30.7 + - - +
321A ALA* 2.9 30.5 + - - +
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Residues in contact with PHE 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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265A SER* 3.2 36.8 - - - -
266A THR* 3.4 18.8 - - - -
269A LEU* 3.9 15.0 - - + -
272A MET* 4.0 5.1 - - + +
286A ALA* 3.8 17.5 - - + -
288A HIS* 3.7 19.5 - + + -
314A SER* 3.3 13.0 - - - -
315A HIS* 3.1 43.9 + + - +
317A GLY* 1.3 77.4 - - - +
319A LEU* 1.3 63.0 + - - +
321A ALA* 3.2 10.6 + - - +
322A GLY 3.3 0.5 + - - -
323A ALA* 3.0 24.8 + - + +
326A ILE* 3.8 28.9 - - + -
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Residues in contact with LEU 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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33A GLU* 5.4 1.6 - - - +
34A ARG* 2.9 57.0 + - + +
35A GLN 3.7 0.9 - - - +
36A LEU* 3.5 42.4 - - + +
40A MET* 4.1 11.2 - - - -
315A HIS 3.7 10.5 - - - +
316A GLN* 3.0 21.7 + - - +
318A PHE* 1.3 76.2 - - - +
320A ARG* 1.3 64.4 + - - +
322A GLY* 3.1 5.0 + - - -
323A ALA 3.2 23.6 - - - +
324A ARG* 4.3 1.6 - - - -
326A ILE* 4.0 21.3 - - + -
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Residues in contact with ARG 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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33A GLU* 4.6 12.7 - - + +
269A LEU* 4.1 19.8 - - - +
273A ARG* 2.7 28.4 + - - -
313A GLU* 5.0 4.0 + - - +
316A GLN* 2.9 24.3 + - + +
317A GLY* 3.5 32.5 + - - +
319A LEU* 1.3 79.1 - - - +
321A ALA* 1.3 50.7 + - - +
322A GLY 3.1 0.7 + - - -
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Residues in contact with ALA 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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269A LEU* 3.6 35.9 - - + +
272A MET* 3.4 12.2 - - + +
273A ARG* 3.3 39.7 + - + +
317A GLY 2.9 17.6 + - - +
318A PHE 3.2 5.3 + - - +
320A ARG* 1.3 78.8 - - - +
322A GLY* 1.3 56.7 + - - +
323A ALA 3.8 0.4 - - - -
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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