Contacts of the helix formed by residues 320 - 333 (chain A) in PDB entry 5K56
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ILE* 3.5 6.3 - - - +
203A LYS 2.8 23.3 + - - -
204A LYS 3.3 10.3 - - - -
205A LYS* 3.8 0.7 - - - -
206A GLY 3.7 4.7 + - - -
259A GLY* 3.7 5.5 - - - -
260A GLY 2.8 28.3 + - - -
319A GLY* 1.3 70.6 - - - -
321A PRO* 1.3 71.8 - - - +
323A ASP* 3.0 33.8 + - - +
324A VAL* 3.1 11.3 + - - +
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Residues in contact with PRO 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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202A ILE* 4.3 1.6 - - + +
203A LYS 3.5 9.0 - - - +
204A LYS* 3.2 24.7 - - + +
292A GLY 3.5 25.1 - - - +
293A GLY* 4.1 1.3 - - - -
294A LEU* 3.6 32.4 - - + +
319A GLY 3.3 3.6 - - - +
320A SER* 1.3 82.6 - - - +
322A GLU* 1.3 57.5 + - + +
324A VAL 3.4 0.2 + - - -
325A GLN* 2.9 39.6 + - - +
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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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204A LYS* 3.0 47.5 + - + +
205A LYS* 3.5 31.9 - - + +
321A PRO* 1.3 77.0 - - + +
323A ASP* 1.3 59.5 + - - +
325A GLN* 3.7 15.4 - - - +
326A GLU* 3.0 33.2 + - - +
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Residues in contact with ASP 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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205A LYS* 3.6 8.4 - - - +
206A GLY* 2.9 27.5 + - - -
226A TYR* 3.4 20.8 + - - +
240A TYR* 2.7 37.2 + - - -
260A GLY* 3.5 10.2 - - - -
261A ILE* 3.9 15.2 - - + +
320A SER* 3.0 18.5 + - - +
322A GLU* 1.3 76.4 - - - +
324A VAL* 1.3 60.1 + - - +
326A GLU* 3.2 9.9 + - - +
327A TYR* 3.0 22.3 + - - +
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Residues in contact with VAL 324 (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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261A ILE* 4.2 12.1 - - + -
294A LEU* 3.8 25.1 - - + +
296A THR* 3.5 30.7 - - + -
317A ILE* 4.4 4.7 - - + +
318A LEU* 3.6 11.4 - - - +
319A GLY 3.4 31.2 - - - +
320A SER 3.1 11.7 + - - +
321A PRO 3.8 3.6 - - - +
323A ASP* 1.3 73.1 - - - +
325A GLN* 1.3 60.6 + - - +
327A TYR* 3.2 3.9 + - - +
328A LEU* 3.0 32.6 + - + +
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Residues in contact with GLN 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 4.0 20.1 - - + +
321A PRO* 2.9 29.1 + - - +
322A GLU* 3.7 16.8 + - - +
323A ASP 3.2 0.2 - - - -
324A VAL* 1.3 73.9 - - - +
326A GLU* 1.3 65.6 + - - +
328A LEU* 3.2 13.7 + - + +
329A THR* 3.0 25.6 + - - -
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Residues in contact with GLU 326 (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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205A LYS* 3.4 27.0 - - - -
226A TYR* 3.8 9.3 - - + -
230A LYS* 3.0 27.7 + - - -
322A GLU* 3.0 20.7 + - + +
323A ASP* 3.2 11.3 + - - +
325A GLN* 1.3 76.7 - - - +
327A TYR* 1.3 63.0 + - - +
329A THR* 3.2 12.5 + - - -
330A CYS* 3.2 21.5 + - - -
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Residues in contact with TYR 327 (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 ASP* 4.4 6.1 + - - -
222A ALA 4.5 2.2 - - - -
223A THR* 3.0 39.3 + - - -
226A TYR* 3.6 30.2 - + + -
261A ILE* 4.2 7.6 - - + -
263A LEU* 3.5 25.1 - - + -
265A PRO* 3.9 11.4 - - - +
296A THR* 4.9 0.4 - - + -
298A GLY* 4.5 6.3 - - - -
317A ILE* 3.8 34.7 - - + +
323A ASP 3.0 12.4 + - - +
324A VAL* 3.2 10.1 + - - +
326A GLU* 1.3 77.6 - - - +
328A LEU* 1.3 64.2 + - + +
330A CYS* 2.9 20.8 + - - +
331A VAL* 3.1 33.9 + - + +
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Residues in contact with LEU 328 (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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294A LEU* 5.5 3.8 - - + -
296A THR* 3.5 34.3 - - + +
298A GLY* 3.6 23.6 - - - +
299A THR* 5.4 1.1 - - - -
324A VAL* 3.0 29.7 + - + +
325A GLN* 3.7 16.8 - - + +
326A GLU 3.2 0.4 - - - -
327A TYR* 1.3 78.4 - - + +
329A THR* 1.3 58.8 + - - +
331A VAL* 3.1 5.9 + - + +
332A GLN* 2.9 44.8 + - + +
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Residues in contact with THR 329 (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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229A LYS* 6.5 1.3 - - - -
325A GLN 3.0 14.0 + - - -
326A GLU* 3.3 13.8 - - - +
328A LEU* 1.3 77.1 - - - +
330A CYS* 1.3 62.5 + - - +
332A GLN* 3.4 12.7 + - - +
333A LYS* 3.1 51.6 + - + +
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Residues in contact with CYS 330 (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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222A ALA* 3.7 21.8 - - + +
225A GLU* 3.6 31.5 - - - +
226A TYR* 3.9 21.1 - - + -
229A LYS* 3.9 23.6 - - - -
326A GLU 3.2 12.2 + - - -
327A TYR 2.9 10.8 + - - +
329A THR* 1.3 80.7 - - - +
331A VAL* 1.3 57.3 + - - +
333A LYS* 3.9 2.2 - - - -
334A ASN* 3.1 30.7 + - - +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP* 6.2 0.2 - - - +
222A ALA* 3.7 17.9 - - + -
298A GLY* 3.6 27.6 - - - +
299A THR* 5.1 7.4 - - + -
327A TYR* 3.1 39.2 + - + +
328A LEU* 3.1 8.3 + - - +
330A CYS* 1.3 75.1 - - - +
332A GLN* 1.3 68.8 - - + +
334A ASN* 3.0 21.0 + - - -
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Residues in contact with GLN 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 2.9 37.3 + - + +
329A THR* 3.9 10.3 + - - +
331A VAL* 1.3 73.7 - - + +
333A LYS* 1.3 71.4 + - + +
334A ASN* 2.9 18.4 + - - +
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Residues in contact with LYS 333 (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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225A GLU* 5.4 3.6 - - - +
329A THR* 3.1 41.6 + - + +
330A CYS* 3.9 2.2 - - - +
332A GLN* 1.3 88.6 + - + +
334A ASN* 1.3 71.1 + - - +
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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