Contacts of the helix formed by residues 303 - 321 (chain A) in PDB entry 4U0Q
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 MET 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A THR* 3.6 39.9 - - + +
237A LYS* 3.7 28.0 - - + -
238A LEU* 3.9 25.8 - - + +
302A LYS* 1.3 75.3 - - - +
304A MET* 1.3 58.4 + - - +
305A ASP 3.4 2.5 - - - +
306A GLU* 3.3 45.4 + - + +
307A TYR* 3.0 27.4 + - - +
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Residues in contact with MET 304 (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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238A LEU* 4.5 7.5 - - - +
302A LYS* 3.6 12.7 - - + -
303A MET* 1.3 76.7 - - - +
305A ASP* 1.4 61.6 + - - +
307A TYR* 3.2 28.6 + - + +
308A ASN* 2.7 51.7 + - - +
412A PHE* 3.5 39.5 - - + -
415A LYS* 6.2 4.0 - - + -
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LYS* 2.7 51.7 + - - +
304A MET* 1.4 73.5 - - - +
306A GLU* 1.4 52.4 + - - +
308A ASN* 4.3 6.1 - - - +
309A THR* 2.7 37.8 + - - +
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Residues in contact with GLU 306 (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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234A THR* 3.5 13.6 + - - +
237A LYS* 4.9 3.1 - - - +
303A MET* 3.3 51.8 + - + +
304A MET 3.2 0.6 - - - -
305A ASP* 1.4 79.0 - - - +
307A TYR* 1.4 61.5 + - - +
309A THR* 3.3 12.6 + - - +
310A LYS* 3.3 43.4 + - + +
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Residues in contact with TYR 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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163A ILE* 6.0 1.7 - - - +
165A GLN* 5.4 3.6 + - - -
231A LEU* 3.9 17.4 - - + +
234A THR* 5.0 5.4 - - - -
235A ILE* 3.9 25.6 - - + -
238A LEU* 3.8 22.4 - - + -
303A MET* 3.0 13.2 + - - +
304A MET* 3.2 28.9 + - + +
306A GLU* 1.4 75.2 - - - +
308A ASN* 1.4 64.3 + - - +
310A LYS* 3.1 4.7 + - - +
311A LYS* 2.8 72.8 + - + +
412A PHE* 4.1 20.2 - + - -
416A GLU* 4.5 14.2 + - + +
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Residues in contact with ASN 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 MET* 2.7 48.2 + - - +
305A ASP* 4.3 6.1 - - - +
307A TYR* 1.4 86.1 - - - +
309A THR* 1.3 58.0 + - + +
311A LYS* 3.9 7.0 + - - +
312A LYS* 3.2 33.3 + - + +
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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
----------------------------------------------------------
305A ASP* 2.7 25.6 + - + +
306A GLU* 3.3 11.3 + - - +
308A ASN* 1.3 77.8 - - + +
310A LYS* 1.4 63.5 + - - +
311A LYS 3.3 0.2 - - - -
312A LYS* 3.3 11.0 + - + +
313A LYS* 2.9 34.5 + - - +
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ILE* 4.2 6.2 - - + +
230A ASP* 2.7 37.9 + - + +
231A LEU* 3.6 25.0 - - + +
234A THR* 3.6 27.5 - - + +
306A GLU* 3.3 39.9 + - - +
307A TYR 3.1 1.6 + - - -
309A THR* 1.4 76.9 + - - +
311A LYS* 1.4 61.7 + - - +
313A LYS* 3.6 13.6 + - + +
314A LEU* 3.4 19.1 + - - +
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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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163A ILE* 5.0 23.4 - - + +
231A LEU* 3.5 22.8 - - + +
307A TYR* 2.8 50.8 + - + +
308A ASN* 4.0 7.6 - - - +
310A LYS* 1.4 75.1 - - - +
312A LYS* 1.4 61.8 + - - +
314A LEU* 3.3 5.1 + - + +
315A ILE* 3.3 43.3 + - + +
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Residues in contact with LYS 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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308A ASN* 3.2 23.7 + - + +
309A THR* 3.4 11.7 - - + +
311A LYS* 1.4 74.3 - - - +
313A LYS* 1.4 53.0 + - - +
315A ILE* 3.4 11.8 + - + +
316A LYS* 2.8 60.8 + - + +
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Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ILE* 3.6 25.6 - - + +
309A THR* 2.9 21.9 + - - +
310A LYS* 3.7 14.1 - - + +
311A LYS 3.3 0.2 - - - -
312A LYS* 1.4 73.5 - - - +
314A LEU* 1.4 57.9 + - - +
316A LYS* 3.6 16.8 - - + +
317A CYS* 3.1 27.0 + - - +
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Residues in contact with LEU 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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163A ILE* 4.5 15.5 - - + -
171A LEU* 3.7 28.9 - - + -
173A PHE* 4.0 18.8 - - + -
224A CYS* 4.3 13.2 - - + +
227A ILE* 3.6 7.6 - - + +
228A LYS* 4.3 22.0 - - + +
231A LEU* 3.8 19.1 - - + -
310A LYS 3.4 8.4 + - - +
311A LYS* 3.3 10.2 + - + +
312A LYS 3.3 0.4 - - - -
313A LYS* 1.4 77.0 - - - +
315A ILE* 1.4 59.1 + - + +
317A CYS* 3.1 7.0 + - - +
318A ILE* 3.0 48.9 + - + +
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Residues in contact with ILE 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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161A ILE* 3.8 24.7 - - + -
163A ILE* 5.0 11.2 - - + -
311A LYS* 3.3 40.0 + - + +
312A LYS* 3.8 11.7 - - + +
314A LEU* 1.4 74.7 - - + +
316A LYS* 1.4 56.1 + - - +
318A ILE* 3.4 12.0 + - + +
319A LYS* 2.9 51.8 + - - +
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Residues in contact with LYS 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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312A LYS* 2.8 44.3 + - - +
313A LYS* 3.6 16.6 - - + +
314A LEU 3.3 0.2 - - - -
315A ILE* 1.4 70.8 - - - +
317A CYS* 1.4 56.2 + - - +
319A LYS* 3.2 10.2 + - + +
320A ASN* 2.8 47.7 + - - +
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Residues in contact with CYS 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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223A LYS 4.0 5.2 - - - -
224A CYS* 2.0 55.9 - - + -
227A ILE* 3.8 17.5 - - + -
313A LYS 3.1 14.0 + - - +
314A LEU* 3.1 9.8 + - - +
316A LYS* 1.4 75.0 - - - +
318A ILE* 1.4 60.0 + - - +
320A ASN* 3.3 17.8 + - - +
321A HIS* 3.3 31.5 + - - -
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Residues in contact with ILE 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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161A ILE* 3.7 36.8 - - + -
163A ILE* 5.3 0.7 - - + -
173A PHE* 3.6 44.2 - - + -
175A ILE* 3.7 29.4 - - + -
224A CYS* 4.3 4.0 - - - -
314A LEU* 3.0 35.7 + - + +
315A ILE* 3.6 9.2 - - + +
316A LYS 3.4 0.2 - - - -
317A CYS* 1.4 73.3 - - - +
319A LYS* 1.4 61.9 + - + +
321A HIS 3.3 9.4 + - - -
322A GLU* 3.5 9.4 + - - +
325A PHE* 3.7 14.6 - - + -
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Residues in contact with LYS 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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161A ILE* 5.3 6.3 - - + -
315A ILE* 2.9 40.0 + - + +
316A LYS* 3.6 10.1 - - + +
318A ILE* 1.4 76.3 - - - +
320A ASN* 1.3 63.4 + - - +
322A GLU* 3.4 26.3 - - - +
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Residues in contact with ASN 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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316A LYS* 2.8 35.6 + - - +
317A CYS* 3.3 11.0 + - - +
319A LYS* 1.3 78.9 - - - +
321A HIS* 1.3 71.2 + - + +
322A GLU 3.3 2.1 + - - -
323A ASN* 4.7 5.2 + - - +
324A ASP* 4.4 3.3 - - - +
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Residues in contact with HIS 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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220A VAL* 3.8 22.6 + - + +
223A LYS* 3.3 46.1 - - + +
224A CYS* 4.7 2.8 - - - -
317A CYS* 3.3 30.0 + - - +
318A ILE* 3.3 1.1 + - - -
319A LYS 3.3 0.6 - - - -
320A ASN* 1.3 88.6 + - + +
322A GLU* 1.4 57.5 + - - +
323A ASN 3.3 2.7 - - - -
324A ASP* 3.2 20.2 + - - +
325A PHE* 3.0 42.8 + - + -
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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