Contacts of the helix formed by residues 339 - 348 (chain A) in PDB entry 5D3O
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 VAL 339 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A LYS* 4.5 0.7 - - - +
319A SER* 4.6 11.0 - - - +
327A PHE 6.0 0.4 - - - +
335A HIS* 4.7 9.9 - - + +
336A ASN* 3.0 41.7 - - - +
338A MET* 1.3 81.8 - - + +
340A ASN* 1.3 55.3 + - - +
341A ALA* 4.2 7.9 - - + +
342A GLY 3.1 12.9 + - - +
343A ALA* 2.8 33.8 + - - +
468A CYS* 5.6 3.4 - - + +
471A TYR* 5.8 5.2 - - + -
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Residues in contact with ASN 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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294A LYS* 2.9 21.1 + - - -
339A VAL* 1.3 73.3 - - - +
341A ALA* 1.3 58.3 + - - +
343A ALA* 3.1 4.0 + - - +
344A ILE* 2.8 36.5 + - + +
392A ARG* 3.8 21.7 - - - +
393A ASN* 3.1 25.6 + - - +
396A ILE* 4.0 15.5 - - + -
419A TYR* 3.3 18.8 + - - +
471A TYR* 5.0 3.3 + - - -
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Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PHE* 4.4 22.2 - - + +
328A LEU* 5.3 0.7 - - + -
334A PRO* 3.7 17.7 - - + -
339A VAL* 3.3 6.6 - - + +
340A ASN* 1.3 76.5 - - - +
342A GLY* 1.3 63.4 + - - +
344A ILE* 3.2 4.6 + - - +
345A VAL* 3.1 26.2 + - - +
396A ILE* 3.7 29.9 - - + +
400A LEU* 4.3 6.3 - - + +
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Residues in contact with GLY 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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314A VAL* 4.1 4.7 - - - +
334A PRO* 3.4 18.4 - - - +
336A ASN 3.4 20.6 - - - -
337A PRO* 3.9 9.2 - - - -
339A VAL* 3.1 6.7 + - - +
341A ALA* 1.3 77.7 - - - +
343A ALA* 1.3 56.8 + - - +
345A VAL* 3.3 2.4 + - - +
346A VAL* 2.9 32.9 + - - +
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Residues in contact with ALA 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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294A LYS* 3.6 33.7 - - + -
297A LYS* 3.9 6.3 - - - +
337A PRO 3.8 6.3 + - - +
339A VAL 2.8 16.3 + - - +
340A ASN 3.5 5.2 - - - +
342A GLY* 1.3 77.7 - - - +
344A ILE* 1.3 56.8 + - - +
346A VAL* 3.5 5.9 + - - +
347A THR* 2.8 33.5 + - - -
419A TYR* 3.6 16.4 - - + -
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Residues in contact with ILE 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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340A ASN 2.8 22.6 + - - +
341A ALA 3.7 3.8 - - - +
343A ALA* 1.3 74.8 - - - +
345A VAL* 1.3 64.9 + - - +
347A THR* 3.4 5.2 + - - -
348A SER* 3.3 16.3 + - - -
393A ASN* 4.1 23.6 - - + +
396A ILE* 4.2 17.0 - - + -
397A GLY* 5.0 2.0 - - - +
400A LEU* 4.2 8.1 - - + -
406A PHE* 3.9 22.7 - - + -
415A ILE* 3.7 15.3 - - + +
416A LEU* 3.9 28.3 - - + -
419A TYR* 3.6 27.8 - - + -
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Residues in contact with VAL 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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313A TYR* 3.6 39.5 - - + +
314A VAL* 4.8 3.4 - - + +
334A PRO* 3.5 31.0 - - + -
341A ALA 3.1 6.9 + - - +
342A GLY* 3.3 6.3 + - - +
344A ILE* 1.3 73.5 - - - +
346A VAL* 1.3 65.4 + - - +
348A SER* 2.6 29.0 + - - +
349A LEU* 3.4 6.5 - - + +
400A LEU* 4.0 15.0 - - + -
405A CYS* 3.9 15.5 - - + +
406A PHE* 4.1 12.3 - - + -
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Residues in contact with VAL 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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297A LYS* 3.6 40.4 - - + +
298A TYR* 4.1 14.1 - - + -
301A ALA* 4.2 6.7 - - + -
310A VAL* 4.8 2.2 - - + -
314A VAL* 4.1 17.5 - - + -
337A PRO* 4.1 22.0 - - + -
342A GLY 2.9 19.9 + - - +
343A ALA* 3.8 5.4 - - - +
345A VAL* 1.3 75.1 - - - +
347A THR* 1.3 67.3 + - - +
349A LEU* 2.8 27.6 + - + +
350A ILE* 3.6 10.4 + - + +
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Residues in contact with THR 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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297A LYS* 3.2 24.0 + - - +
343A ALA 2.8 22.0 + - - -
344A ILE* 3.5 9.6 - - - -
346A VAL* 1.3 79.1 - - - +
348A SER* 1.3 60.5 + - - +
349A LEU 3.4 0.7 + - - -
350A ILE* 3.7 16.8 + - - +
359A LYS* 5.7 0.2 - - - +
415A ILE* 4.0 20.0 - - + +
418A PHE* 3.4 44.9 - - + -
419A TYR* 3.6 13.1 - - + +
422A LEU* 4.2 3.6 - - + -
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Residues in contact with SER 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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344A ILE 3.3 5.5 + - - -
345A VAL* 2.6 18.4 + - - +
346A VAL 2.9 1.4 + - - -
347A THR* 1.3 79.2 - - - +
349A LEU* 1.3 58.7 + - - +
350A ILE 4.5 1.6 - - - +
352A GLN* 3.7 15.2 - - - +
359A LYS* 5.5 2.0 + - - -
406A PHE* 3.3 33.5 - - - -
407A PRO* 3.3 17.7 - - - +
410A THR* 4.3 7.7 + - - +
415A ILE* 3.6 25.9 - - - +
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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