Contacts of the helix formed by residues 338 - 350 (chain A) in PDB entry 3AP1
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A LEU 3.0 18.0 + - - +
244A HIS* 2.7 45.8 + - - +
245A PRO* 3.9 3.3 - - - +
246A ARG* 4.5 9.9 + - - +
247A ARG* 5.2 1.7 + - - +
337A PRO* 1.3 75.0 - - - +
339A PRO* 1.3 76.1 - - + +
340A PHE* 4.0 12.1 - - + +
341A VAL* 3.0 20.1 + - + +
342A ILE* 3.1 9.4 + - - +
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Residues in contact with PRO 339 (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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337A PRO 3.7 4.0 - - - +
338A ASP* 1.3 84.4 - - + +
340A PHE* 1.3 52.9 + - - +
342A ILE* 3.0 16.6 + - + +
343A ASN* 2.8 48.4 + - - +
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Residues in contact with PHE 340 (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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245A PRO* 3.9 27.1 - - + -
246A ARG* 5.7 3.8 - - + -
265A LEU* 3.2 47.8 - - + -
266A HIS* 4.3 17.9 - + - -
268A GLU* 6.1 0.4 - - - -
293A VAL* 5.4 2.9 - - + -
338A ASP* 3.1 9.8 + - + +
339A PRO* 1.3 78.6 - - - +
341A VAL* 1.3 58.2 + - - +
343A ASN* 3.5 9.1 + - + +
344A ASN* 3.0 62.4 + - - +
347A ARG* 5.9 0.4 - - - -
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL 3.2 28.9 - - - +
243A LEU 3.6 9.4 - - - +
245A PRO* 3.4 27.6 - - + -
293A VAL* 3.5 19.7 - - + +
294A ASN* 3.9 7.6 - - - -
295A LEU* 3.8 26.0 - - + -
337A PRO* 4.5 1.6 - - + -
338A ASP* 3.0 10.4 + - + +
340A PHE* 1.3 74.3 - - + +
342A ILE* 1.3 66.7 + - - +
344A ASN* 3.7 5.8 - - - +
345A THR* 2.8 30.0 + - - -
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Residues in contact with ILE 342 (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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295A LEU* 4.4 9.6 - - + -
337A PRO* 3.7 37.7 - - + +
338A ASP 3.1 9.5 + - - +
339A PRO* 3.0 18.9 + - + +
341A VAL* 1.3 75.6 - - - +
343A ASN* 1.3 69.0 + - - +
345A THR* 3.2 4.1 + - - -
346A GLN* 3.0 35.3 + - + +
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Residues in contact with ASN 343 (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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339A PRO* 2.8 29.3 + - - +
340A PHE* 3.7 8.1 - - + +
342A ILE* 1.3 83.1 - - - +
344A ASN* 1.3 62.1 + - - +
346A GLN* 3.2 8.8 + - - +
347A ARG* 3.0 36.2 + - + +
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Residues in contact with ASN 344 (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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265A LEU 5.2 0.4 + - - -
292A PRO* 3.8 21.6 - - + +
293A VAL* 3.1 32.0 + - - +
294A ASN* 4.6 0.2 - - - -
340A PHE* 3.0 58.3 + - - +
341A VAL* 3.7 5.2 - - - +
343A ASN* 1.3 75.5 - - - +
345A THR* 1.3 61.6 + - - +
347A ARG* 3.1 32.0 + - - +
348A VAL* 3.0 27.4 + - - +
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Residues in contact with THR 345 (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 ASN* 3.5 9.7 - - + +
295A LEU* 3.0 45.4 + - + +
296A GLU* 4.4 17.3 - - + +
341A VAL 2.8 21.3 + - - -
342A ILE* 3.5 5.8 - - - -
344A ASN* 1.3 74.5 - - - +
346A GLN* 1.3 61.5 + - - +
348A VAL* 3.3 4.9 + - - +
349A LEU* 3.0 43.0 + - + +
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Residues in contact with GLN 346 (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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342A ILE* 3.0 28.7 + - + +
343A ASN* 3.6 10.5 - - - +
345A THR* 1.3 79.3 - - - +
347A ARG* 1.3 56.6 + - + +
349A LEU* 3.3 25.4 + - - +
350A LYS* 3.0 51.9 + - - +
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Residues in contact with ARG 347 (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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268A GLU* 3.6 15.8 + - - -
292A PRO* 4.0 6.7 - - - +
340A PHE* 5.9 0.6 - - - -
343A ASN* 3.0 20.2 + - + +
344A ASN* 3.1 41.9 + - - +
346A GLN* 1.3 76.4 - - + +
348A VAL* 1.3 62.1 + - - +
350A LYS* 3.4 11.3 + - + +
351A GLY 3.3 4.5 + - - -
352A ASP* 3.2 47.4 + - - +
353A TYR* 2.8 31.4 + - + -
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Residues in contact with VAL 348 (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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291A LYS* 3.5 31.9 - - + +
292A PRO* 3.8 28.0 - - + -
294A ASN* 4.3 13.9 - - + +
296A GLU* 3.7 22.2 - - - +
344A ASN 3.0 17.5 + - - +
345A THR* 3.4 9.0 - - - +
347A ARG* 1.3 75.7 - - - +
349A LEU* 1.3 58.2 + - - +
351A GLY* 2.9 20.6 + - - -
353A TYR* 4.1 11.8 + - + -
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Residues in contact with LEU 349 (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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296A GLU* 3.7 31.9 - - + +
345A THR* 3.0 32.3 + - + +
346A GLN* 3.8 29.8 - - - +
348A VAL* 1.3 76.1 - - + +
350A LYS* 1.3 61.2 + - + +
351A GLY* 3.1 1.1 + - - -
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Residues in contact with LYS 350 (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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346A GLN* 3.0 38.9 + - - +
347A ARG* 3.6 13.9 - - + +
348A VAL 3.2 0.6 - - - -
349A LEU* 1.3 77.4 - - + +
351A GLY* 1.3 58.9 + - - +
352A ASP* 3.6 12.3 - - - +
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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