Contacts of the helix formed by residues 392 - 398 (chain A) in PDB entry 2YD0
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 PRO 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A VAL 4.0 0.4 - - - +
388A SER* 4.1 17.7 - - - +
389A VAL 3.4 14.8 - - - +
390A THR 3.5 4.5 - - - +
391A HIS* 1.3 88.7 - - - +
393A GLU* 1.3 63.0 + - - +
395A LYS* 3.0 30.7 + - - +
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Residues in contact with GLU 393 (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 LYS* 4.3 13.3 + - - +
390A THR 5.2 0.2 - - - +
391A HIS* 3.2 42.1 - - - +
392A PRO* 1.3 80.2 - - - +
394A LEU* 1.3 68.0 + - + +
395A LYS* 3.3 5.2 + - - +
721A SER* 5.2 6.1 - - - -
722A VAL* 4.7 13.0 + - + +
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Residues in contact with LEU 394 (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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281A TYR* 4.5 1.6 - - - +
344A LYS* 4.1 19.3 - - + +
345A LEU* 4.2 23.6 - - + +
348A THR* 3.8 24.9 - - - +
387A VAL* 3.9 12.3 - - + -
391A HIS* 3.0 31.9 + - + +
393A GLU* 1.3 81.4 - - + +
395A LYS* 1.3 69.2 + - - +
396A VAL* 3.1 13.7 + - + -
399A TYR* 3.5 21.5 + - - -
722A VAL* 3.7 34.4 - - + +
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Residues in contact with LYS 395 (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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388A SER* 6.1 1.8 - - - +
391A HIS 4.2 0.8 + - - -
392A PRO* 3.0 22.2 + - - +
393A GLU* 4.6 5.8 - - - +
394A LEU* 1.3 78.8 - - - +
396A VAL* 1.3 64.8 + - - +
397A GLY 3.0 4.9 + - - -
398A ASP* 3.1 36.6 + - - +
399A TYR* 4.1 5.0 - - - +
723A SER* 6.3 2.7 - - - -
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Residues in contact with VAL 396 (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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345A LEU* 4.0 10.8 - - + -
349A MET* 3.8 22.4 - - + -
384A PHE* 3.7 26.6 - - + +
387A VAL* 3.7 25.8 - - + -
388A SER* 3.8 31.8 - - - +
391A HIS 5.5 0.2 - - - +
394A LEU* 3.1 16.8 + - + -
395A LYS* 1.3 74.6 - - - +
397A GLY* 1.3 60.7 - - - +
398A ASP 3.3 0.2 - - - -
399A TYR* 2.9 33.2 + - + +
400A PHE 3.5 6.8 + - - -
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Residues in contact with GLY 397 (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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384A PHE* 4.8 3.8 - - - -
388A SER* 4.8 7.0 - - - -
395A LYS 3.0 1.8 + - - -
396A VAL* 1.3 80.9 - - - +
398A ASP* 1.3 65.2 + - - +
399A TYR 3.1 0.9 + - - -
400A PHE* 3.3 19.7 + - - +
634A ASN* 4.1 8.4 + - - -
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Residues in contact with ASP 398 (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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395A LYS* 3.1 30.9 + - - +
397A GLY* 1.3 76.2 - - - +
399A TYR* 1.4 70.9 + - + +
401A PHE* 5.0 0.9 + - - +
634A ASN* 3.3 28.8 + - - +
670A ILE* 5.4 7.0 - - + +
671A MET* 3.4 14.7 - - + +
723A SER* 5.3 6.2 + - - -
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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