Contacts of the helix formed by residues 351 - 359 (chain A) in PDB entry 1YHV
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 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A GLY 4.6 0.5 - - - +
350A GLY* 1.3 74.6 - - - -
352A LEU* 1.3 65.9 + - - +
353A THR* 3.3 21.1 + - - -
354A ASP* 3.1 29.2 + - - +
355A VAL* 3.5 7.3 + - - +
392A SER 4.0 5.6 - - - -
393A ASP* 4.2 7.6 - - - -
395A ILE 3.2 11.9 - - - -
396A LEU* 4.0 13.2 - - - -
397A LEU* 3.8 11.1 - - - +
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Residues in contact with LEU 352 (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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351A SER* 1.3 72.1 - - - +
353A THR* 1.3 63.5 + - - +
355A VAL* 3.0 9.3 + - + +
356A VAL* 2.9 36.5 + - + +
361A MET* 4.4 9.0 - - + -
369A VAL* 4.0 30.1 - - + -
392A SER* 3.4 15.7 + - - +
395A ILE* 2.8 23.9 + - + -
397A LEU* 4.0 13.6 - - + +
453A MET* 3.7 38.6 - - + -
457A MET* 4.2 19.3 - - + -
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Residues in contact with THR 353 (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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351A SER* 3.1 8.0 - - - -
352A LEU* 1.3 78.7 - - - +
354A ASP* 1.3 63.3 + - - +
356A VAL* 3.3 4.7 + - + -
357A THR* 2.8 44.7 + - + +
392A SER* 2.6 26.4 + - - +
393A ASP* 2.8 36.9 + - - +
456A GLU* 5.2 0.9 - - - +
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Residues in contact with ASP 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLY 5.7 0.9 - - - +
350A GLY* 3.8 8.1 - - - -
351A SER* 3.1 34.5 + - - +
353A THR* 1.3 79.5 - - - +
355A VAL* 1.3 62.9 + - + +
357A THR* 3.8 4.9 - - - -
358A GLU* 3.0 32.7 + - - +
537A ALA* 3.5 15.4 - - + +
538A LYS* 6.0 0.4 - - - -
541A THR 3.9 23.1 - - - +
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLY 5.5 1.1 - - - +
351A SER 3.5 2.4 + - - +
352A LEU* 3.0 14.3 + - + +
354A ASP* 1.3 77.1 - - + +
356A VAL* 1.3 57.5 + - - +
359A THR* 2.6 47.8 + - - +
361A MET* 3.9 29.4 - - + -
397A LEU* 3.7 26.0 - - + -
530A LEU* 6.4 0.2 - - + -
533A LEU* 4.1 26.0 - - + +
534A ILE* 4.1 14.8 - - + +
537A ALA* 3.9 8.1 - - + -
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 2.9 33.1 + - + +
353A THR* 3.5 16.2 - - + +
355A VAL* 1.3 74.2 - - - +
357A THR* 1.3 69.1 + - + +
359A THR 3.8 10.9 - - - +
361A MET* 4.4 6.1 - - - -
392A SER* 4.6 0.4 - - - +
456A GLU* 3.6 32.1 - - + +
457A MET* 3.7 37.7 - - + +
460A GLY* 3.8 24.6 - - - +
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Residues in contact with THR 357 (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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353A THR* 2.8 33.8 + - + +
354A ASP* 3.4 8.3 + - - -
356A VAL* 1.3 83.2 - - + +
358A GLU* 1.3 76.9 + - - +
359A THR 5.0 0.2 - - - -
460A GLY* 4.0 16.8 - - - +
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Residues in contact with GLU 358 (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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354A ASP* 3.0 21.7 + - - +
357A THR* 1.3 94.1 + - - +
359A THR* 1.3 61.6 + - + +
536A ALA* 5.2 0.4 - - - +
537A ALA* 4.0 20.6 - - + +
540A ALA* 3.6 39.3 - - + +
541A THR 5.0 3.3 - - - -
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Residues in contact with THR 359 (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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355A VAL* 2.6 41.1 + - - +
356A VAL* 3.8 12.1 - - - +
357A THR 5.0 0.2 - - - -
358A GLU* 1.3 84.9 - - + +
360A CYS* 1.3 62.5 + - - +
361A MET* 4.0 1.6 + - - +
533A LEU* 3.6 44.0 - - + +
536A ALA* 4.1 16.2 - - + -
537A ALA* 4.2 6.5 - - + +
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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