Contacts of the helix formed by residues 338 - 351 (chain C) in PDB entry 3AP3
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 338 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243C LEU 3.3 11.8 + - - -
244C HIS* 3.6 22.8 + - - +
245C PRO* 3.4 18.7 - - + +
246C ARG* 4.4 9.7 + - - +
247C ARG* 5.1 1.7 + - - +
336C ASN 3.7 0.7 + - - +
337C PRO* 1.3 75.0 - - - +
339C PRO* 1.4 67.2 - - + +
340C PHE* 3.0 11.8 - - + +
341C VAL* 2.9 31.4 + - + +
342C ILE* 3.1 10.3 + - - +
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Residues in contact with PRO 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C PRO 3.7 4.4 - - - +
338C ASP* 1.4 87.8 - - + +
340C PHE* 1.3 55.1 + - - +
342C ILE* 3.9 15.3 - - + -
343C ASN* 3.1 42.1 + - - +
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Residues in contact with PHE 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C PRO* 3.3 33.2 - - + -
246C ARG* 5.8 1.8 - - + -
265C LEU* 3.2 54.5 - - + -
266C HIS* 4.6 14.4 - + - -
268C GLU* 6.1 0.2 - - - -
293C VAL* 5.2 3.6 - - + -
338C ASP* 3.0 9.8 - - + +
339C PRO* 1.3 80.1 - - - +
341C VAL* 1.3 56.3 + - - +
343C ASN* 4.2 3.5 - - - +
344C ASN* 2.9 61.3 + - - +
347C ARG* 5.5 2.7 - - - -
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Residues in contact with VAL 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C VAL* 3.0 22.7 - - + +
243C LEU 3.1 26.9 - - - +
245C PRO* 3.3 19.7 - - + -
293C VAL* 3.3 27.1 - - + +
295C LEU* 3.8 23.8 - - + -
337C PRO* 4.7 0.2 - - + -
338C ASP* 2.9 12.5 + - + +
340C PHE* 1.3 72.5 - - - +
342C ILE* 1.3 57.4 + - - +
344C ASN* 3.4 6.8 + - - +
345C THR* 2.6 37.4 + - - -
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Residues in contact with ILE 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C LEU* 4.0 7.6 - - + -
337C PRO* 3.6 37.9 - - + +
338C ASP 3.1 13.2 + - - +
339C PRO* 3.9 16.4 - - + +
341C VAL* 1.3 75.9 - - - +
343C ASN* 1.3 62.6 + - - +
345C THR* 3.1 11.2 + - - -
346C GLN* 3.0 39.0 + - + +
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Residues in contact with ASN 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C PRO* 3.1 27.9 + - - +
340C PHE* 4.2 5.3 - - + +
342C ILE* 1.3 79.4 - - - +
344C ASN* 1.3 65.8 + - - +
346C GLN* 3.5 11.9 - - - +
347C ARG* 3.2 31.2 + - - +
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Residues in contact with ASN 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C LEU 5.3 0.4 + - - -
292C PRO* 4.0 16.9 - - + +
293C VAL* 3.5 26.1 + - - +
340C PHE* 2.9 52.3 + - - +
341C VAL* 3.5 8.6 - - - +
342C ILE 3.2 0.4 - - - -
343C ASN* 1.3 75.1 - - - +
345C THR* 1.3 65.2 + - - +
347C ARG* 2.9 51.2 + - - +
348C VAL* 3.0 17.5 + - - +
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Residues in contact with THR 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C ASN* 4.1 9.8 - - - +
295C LEU* 3.3 37.0 + - + +
296C GLU* 3.9 27.4 - - + -
341C VAL 2.6 20.2 + - - -
342C ILE* 3.1 9.6 + - - -
344C ASN* 1.3 74.8 - - - +
346C GLN* 1.3 58.6 + - - +
348C VAL* 3.5 3.8 + - - +
349C LEU* 3.1 45.1 + - + +
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Residues in contact with GLN 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C ILE* 3.0 29.3 + - + +
343C ASN* 3.5 14.6 - - - +
344C ASN 3.0 0.2 - - - -
345C THR* 1.3 74.8 - - - +
347C ARG* 1.3 66.3 + - + +
348C VAL 3.0 1.8 - - - -
349C LEU* 3.0 31.5 + - - +
350C LYS* 3.0 43.2 + - - +
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Residues in contact with ARG 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C GLU* 4.0 12.3 + - - +
292C PRO* 3.5 27.4 - - + +
340C PHE* 5.5 3.4 - - - -
343C ASN* 3.2 15.7 + - - +
344C ASN* 2.9 44.2 + - - +
346C GLN* 1.3 75.6 - - + +
348C VAL* 1.3 58.0 + - + +
350C LYS* 3.3 9.6 + - + +
351C GLY 3.1 6.9 + - - -
352C ASP* 2.8 59.5 + - + +
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C LYS* 3.7 35.0 - - + +
292C PRO* 3.7 32.1 - - + -
294C ASN* 4.7 11.2 - - + -
296C GLU* 3.4 22.9 - - - +
344C ASN 3.0 14.1 + - - +
345C THR* 3.6 9.6 - - - +
346C GLN 3.0 0.2 - - - -
347C ARG* 1.3 73.5 - - - +
349C LEU* 1.3 57.9 + - - +
350C LYS 3.1 4.7 - - - -
351C GLY* 3.1 17.4 + - - +
352C ASP* 4.6 6.7 - - + +
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Residues in contact with LEU 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C GLU* 3.3 30.1 - - + +
345C THR* 3.1 33.1 + - + +
346C GLN* 3.0 23.8 + - - +
348C VAL* 1.3 75.0 - - - +
350C LYS* 1.3 60.2 + - + +
351C GLY 3.5 0.2 - - - -
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Residues in contact with LYS 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C GLN* 3.0 45.8 + - - +
347C ARG* 3.6 13.1 - - + +
348C VAL 3.1 0.2 - - - -
349C LEU* 1.3 81.8 - - - +
351C GLY* 1.3 58.1 + - - +
352C ASP* 3.8 7.7 - - - +
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Residues in contact with GLY 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C ARG 3.1 2.0 + - - -
348C VAL 3.1 11.2 + - - -
349C LEU 3.5 0.2 - - - -
350C LYS* 1.3 79.6 - - - +
352C ASP* 1.3 67.9 + - - +
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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