Contacts of the helix formed by residues 306 - 322 (chain A) in PDB entry 3W0A
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 SER 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A VAL* 5.9 6.5 - - - -
301A THR* 5.1 1.3 - - - -
304A GLY 5.4 0.7 - - - -
305A HIS* 1.3 74.1 - - - +
307A LEU* 1.4 58.7 + - - +
308A GLU* 3.7 18.0 + - - +
309A LEU* 2.9 20.4 + - - -
310A ILE* 3.3 17.1 + - - +
400A GLN* 2.8 35.5 + - - +
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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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297A VAL* 5.0 10.3 - - + -
301A THR* 4.2 22.2 - - + -
306A SER* 1.4 72.0 - - - +
308A GLU* 1.4 62.7 + - + +
309A LEU 3.1 1.4 + - - -
310A ILE* 4.5 6.3 - - + +
311A GLU* 3.1 60.2 + - + +
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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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306A SER* 3.1 12.6 + - - -
307A LEU* 1.4 75.1 - - - +
309A LEU* 1.4 56.2 + - - +
312A PRO* 3.2 20.9 - - - +
396A GLU* 3.4 36.3 - - - +
400A GLN* 3.9 1.9 + - - +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A MET* 4.2 13.2 - - + -
300A VAL* 5.0 2.5 - - + -
305A HIS* 3.4 32.3 - - + +
306A SER 2.9 6.1 + - - +
308A GLU* 1.4 77.2 - - - +
310A ILE* 1.3 59.5 + - + +
311A GLU 3.5 0.4 - - - -
312A PRO* 3.4 5.8 - - - +
313A LEU* 3.0 31.4 + - + +
393A LEU* 3.6 30.9 - - + +
396A GLU* 3.9 6.7 - - + -
397A HIS* 3.8 20.2 - - + +
400A GLN* 3.4 21.5 - - - +
501A DS5 3.9 24.2 - - + -
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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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286A TRP* 5.4 1.6 - - + -
297A VAL* 3.6 42.8 - - + +
300A VAL* 3.8 28.0 - - + -
301A THR* 3.3 47.1 - - + +
305A HIS* 4.3 4.9 - - + +
306A SER 3.3 18.7 + - - +
307A LEU* 4.5 4.3 - - + +
309A LEU* 1.3 74.4 - - + +
311A GLU* 1.4 59.8 + - - +
313A LEU* 3.2 10.2 + - + +
314A ILE* 2.9 35.6 + - + +
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Residues in contact with GLU 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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297A VAL* 6.0 2.2 - - + +
307A LEU* 3.1 48.5 + - + +
310A ILE* 1.4 77.2 - - - +
312A PRO* 1.4 70.6 - - + +
314A ILE* 3.2 5.1 + - - +
315A LYS* 3.1 18.8 + - - +
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Residues in contact with PRO 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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307A LEU 3.8 1.1 - - - +
308A GLU* 3.2 25.8 - - - +
309A LEU* 3.4 10.1 - - - +
311A GLU* 1.4 94.6 - - + +
313A LEU* 1.4 53.7 + - - -
315A LYS* 3.4 12.2 + - + +
316A PHE* 2.8 30.5 + - - +
393A LEU* 3.8 15.3 - - + +
396A GLU* 5.9 1.1 - - + -
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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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272A MET* 4.0 35.9 - - + -
286A TRP* 4.1 11.9 - - + -
300A VAL* 5.4 3.6 - - + -
309A LEU* 3.0 23.0 + - + +
310A ILE* 3.4 15.3 - - + +
311A GLU 3.2 0.6 - - - -
312A PRO* 1.4 74.8 - - - +
314A ILE* 1.3 57.8 + - + +
316A PHE* 3.3 6.3 + - + +
317A GLN* 3.0 51.4 + - + +
393A LEU* 3.7 7.4 - - + +
501A DS5 4.0 38.4 - - + -
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Residues in contact with ILE 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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279A PHE* 3.7 22.7 - - + -
284A MET* 3.9 23.6 - - + +
286A TRP* 3.5 32.8 - - + -
297A VAL* 3.7 25.8 - - + +
310A ILE* 2.9 23.7 + - + +
311A GLU* 3.2 5.1 + - - +
313A LEU* 1.3 72.3 - - - +
315A LYS* 1.4 64.5 + - - +
317A GLN* 3.2 4.0 + - - +
318A VAL* 3.0 30.3 + - + +
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Residues in contact with LYS 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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311A GLU 3.1 13.3 + - - +
312A PRO* 3.5 14.8 - - + +
314A ILE* 1.4 75.9 - - - +
316A PHE* 1.4 57.7 + - - +
318A VAL* 3.4 6.2 + - - +
319A GLY* 2.9 26.0 + - - -
389A ASP* 5.6 4.9 + - - -
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Residues in contact with PHE 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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272A MET* 4.4 6.5 - - + -
273A LEU* 3.9 16.2 - - + -
312A PRO 2.8 17.9 + - - +
313A LEU* 3.4 6.3 - - + +
315A LYS* 1.4 76.1 - - - +
317A GLN* 1.4 72.5 + - - +
319A GLY* 3.2 2.6 + - - +
320A LEU* 2.8 56.6 + - + +
386A LYS* 3.5 44.9 - - + +
389A ASP* 3.9 17.0 - - + +
390A LEU* 3.7 26.9 - - + -
393A LEU* 3.7 25.1 - - + -
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Residues in contact with GLN 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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272A MET 3.0 23.8 + - - -
275A SER* 3.3 10.8 + - - -
276A ASN* 2.9 46.0 + - - +
279A PHE* 3.7 25.9 - - + +
286A TRP* 3.6 24.0 - - + +
313A LEU* 3.0 35.6 + - + +
314A ILE* 3.2 7.6 + - - +
316A PHE* 1.4 86.1 - - - +
318A VAL* 1.3 58.0 + - - +
321A LYS* 2.9 26.5 + - - +
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 3.9 10.1 - - + -
281A MET* 3.7 24.2 - - + -
284A MET* 3.6 35.4 - - + -
314A ILE* 3.0 23.2 + - + +
315A LYS* 3.9 4.7 - - - +
317A GLN* 1.3 73.5 - - - +
319A GLY* 1.3 65.2 + - - +
321A LYS* 3.2 6.3 + - - +
322A LYS* 3.0 36.5 + - + +
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Residues in contact with GLY 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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315A LYS 2.9 15.1 + - - -
316A PHE* 3.6 3.6 - - - -
318A VAL* 1.3 77.4 - - - +
320A LEU* 1.3 62.0 - - - +
322A LYS* 3.6 8.7 + - - +
323A LEU* 3.6 18.5 + - - +
386A LYS* 3.4 21.7 + - - -
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Residues in contact with LEU 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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273A LEU* 3.8 19.5 - - + +
276A ASN* 3.6 32.9 - - + +
316A PHE* 2.8 39.7 + - + +
317A GLN 3.9 3.4 - - - +
319A GLY* 1.3 74.3 - - - +
321A LYS* 1.3 66.2 + - - +
323A LEU* 3.1 29.3 + - + +
324A ASN 4.0 1.4 + - - -
325A LEU* 3.9 28.7 + - + +
330A HIS* 5.6 4.3 - - - +
333A LEU* 4.3 13.7 - - + -
386A LYS* 3.5 17.4 - - + +
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Residues in contact with LYS 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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276A ASN* 2.9 36.8 + - - +
277A GLU* 3.6 12.9 + - - +
279A PHE* 2.8 32.1 + - + +
280A THR* 5.0 2.7 - - - +
281A MET* 4.0 27.1 - - + +
317A GLN 2.9 17.7 + - - +
318A VAL* 3.2 5.1 + - - +
320A LEU* 1.3 75.1 - - - +
322A LYS* 1.4 57.6 + - - +
324A ASN* 3.1 30.5 + - - +
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A MET* 4.0 23.8 - - + -
318A VAL* 3.0 36.2 + - + +
319A GLY* 3.9 8.1 - - - +
320A LEU 3.2 0.2 - - - -
321A LYS* 1.4 71.4 - - - +
323A LEU* 1.4 56.5 + - + +
324A ASN* 3.1 24.8 - - - +
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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