Contacts of the helix formed by residues 320 - 331 (chain A) in PDB entry 1P9B
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 ILE 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A LEU* 4.9 1.6 - - + -
319A ASP* 1.3 67.9 - - - +
321A PRO* 1.3 69.5 - - + +
322A MET 3.1 2.0 - - - -
323A LEU* 3.0 24.7 + - + +
324A LEU* 3.0 23.9 + - + +
351A LEU* 3.5 34.1 - - + -
352A CYS 2.9 24.7 + - - +
353A VAL* 4.2 13.5 - - + +
413A ILE* 4.6 11.4 - - + -
416A TYR* 4.1 23.8 - - + -
417A LEU* 4.1 27.1 - - + -
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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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319A ASP* 3.1 9.9 - - - +
320A ILE* 1.3 92.1 - - + +
322A MET* 1.3 61.6 + - - +
324A LEU* 3.2 13.9 + - + +
325A TYR* 3.1 21.7 + - - +
352A CYS 3.3 14.6 - - - +
353A VAL 3.9 4.5 - - - +
354A ASN* 3.9 22.4 - - - +
355A PHE* 3.7 29.8 - - + -
364A LEU* 4.7 8.5 - - + -
366A LYS* 6.5 0.7 - - - -
367A GLY 5.1 3.0 + - - +
368A CYS 4.4 5.1 - - - +
369A TYR* 3.9 7.4 - - + -
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Residues in contact with MET 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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22A ALA 4.2 4.3 - - - +
23A GLN* 3.9 28.7 - - - -
24A TRP* 3.4 45.1 - - + -
235A MET* 3.7 32.3 - - + -
278A LEU* 3.9 16.4 - - + -
319A ASP* 2.8 27.7 + - - +
321A PRO* 1.3 73.6 - - - +
323A LEU* 1.3 59.0 + - + +
325A TYR* 3.1 6.9 + - - +
326A VAL* 2.9 29.8 + - - +
369A TYR* 3.5 26.8 - - + +
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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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22A ALA* 3.8 34.5 - - + +
23A GLN* 4.3 9.6 - - + +
274A VAL* 3.9 30.3 - - + -
318A LEU* 4.1 13.0 - - + -
319A ASP 3.3 16.4 - - - +
320A ILE* 3.0 17.4 + - + +
322A MET* 1.3 77.9 - - + +
324A LEU* 1.3 59.8 + - - +
326A VAL* 3.7 3.3 - - - +
327A LYS* 2.8 30.0 + - - +
332A ILE* 5.4 1.2 - - - +
413A ILE* 5.3 0.9 - - + -
417A LEU* 3.6 33.1 - - + +
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Residues in contact with LEU 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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320A ILE* 3.0 26.3 + - + +
321A PRO* 3.2 13.0 + - + +
323A LEU* 1.3 77.0 - - - +
325A TYR* 1.3 62.8 + - - +
327A LYS* 3.4 28.5 + - - +
328A CYS* 3.1 28.0 + - - -
353A VAL 6.2 0.2 - - - +
366A LYS* 4.2 36.8 - - + -
367A GLY* 4.3 12.6 - - - +
416A TYR 3.6 23.3 - - - +
417A LEU* 3.7 14.4 - - + -
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Residues in contact with TYR 325 (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 ALA 5.9 0.2 - - - -
235A MET* 3.7 31.4 - - + -
240A PHE* 2.8 49.5 + + + +
321A PRO 3.1 11.8 + - - +
322A MET 3.1 8.9 + - - +
324A LEU* 1.3 78.0 - - - +
326A VAL* 1.3 63.9 + - + +
328A CYS* 3.1 17.5 + - + +
329A ILE* 3.2 26.0 + - + +
367A GLY 3.5 26.2 + - - +
368A CYS* 5.5 0.2 - - - -
369A TYR* 3.7 26.9 - - + -
371A VAL* 4.0 13.7 - - + +
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Residues in contact with VAL 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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22A ALA* 3.2 40.2 - - + +
234A ALA* 3.8 18.8 - - + -
235A MET* 4.0 16.4 - - - -
322A MET 2.9 19.7 + - - +
323A LEU* 3.8 7.2 - - - +
325A TYR* 1.3 75.7 - - + +
327A LYS* 1.3 58.6 + - - +
329A ILE* 3.1 6.4 + - + +
330A ASN* 2.7 58.4 + - + +
332A ILE* 4.5 6.3 - - + -
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Residues in contact with LYS 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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323A LEU 2.8 18.7 + - - +
324A LEU* 3.6 29.2 - - + +
326A VAL* 1.3 76.2 - - - +
328A CYS* 1.3 61.1 + - - +
331A SER* 2.8 29.1 + - - -
332A ILE* 3.8 32.3 - - + +
416A TYR 5.1 0.2 + - - -
417A LEU* 3.1 32.7 + - + +
418A LYS* 4.5 13.5 - - - +
419A THR* 3.8 9.6 - - - +
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Residues in contact with CYS 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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324A LEU 3.1 24.6 + - - -
325A TYR* 3.1 11.1 + - + +
327A LYS* 1.3 84.9 - - - +
329A ILE* 1.3 65.6 + - + +
331A SER* 4.6 1.0 + - - -
367A GLY* 4.3 21.8 - - - +
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Residues in contact with ILE 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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234A ALA* 6.1 0.4 - - + -
240A PHE* 3.6 48.5 - - + -
252A THR* 3.5 34.3 - - + -
253A VAL* 3.6 14.1 - - + +
325A TYR* 3.2 27.3 + - + +
326A VAL* 3.1 9.1 + - + +
328A CYS* 1.3 84.6 - - + +
330A ASN* 1.3 62.7 + - - +
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Residues in contact with ASN 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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20A LEU* 3.8 27.7 + - + +
21A GLY 4.3 3.2 + - - -
234A ALA* 3.8 14.3 - - - +
251A THR 4.9 0.8 + - - -
252A THR* 2.9 18.2 - - - +
253A VAL* 2.7 50.4 + - - +
270A VAL* 4.3 2.6 - - + +
326A VAL* 2.7 33.6 + - - +
329A ILE* 1.3 75.7 - - - +
331A SER* 1.3 82.1 + - - +
332A ILE* 4.1 7.0 - - + +
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Residues in contact with SER 331 (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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270A VAL* 3.6 21.1 - - - +
327A LYS* 2.8 23.7 + - - -
328A CYS 4.5 1.1 - - - -
329A ILE 3.6 0.8 - - - -
330A ASN* 1.3 95.3 + - - +
332A ILE* 1.3 73.5 + - - +
333A ASP* 4.8 6.4 + - - -
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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