Contacts of the helix formed by residues 511 - 519 (chain A) in PDB entry 2DDH
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 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505A HIS 5.1 0.2 - - - +
506A VAL* 4.8 0.6 - - - -
509A ARG* 2.7 14.4 + - - +
510A LYS* 1.3 74.5 - - - +
512A LYS* 1.3 58.4 + - - +
513A GLU* 3.4 13.5 + - - +
514A VAL* 3.2 36.5 + - - +
515A ALA* 2.9 28.3 + - - +
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Residues in contact with LYS 512 (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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502A LEU* 4.8 1.4 - - - +
506A VAL* 4.1 27.4 - - + -
510A LYS 3.2 3.9 + - - +
511A SER* 1.3 72.5 + - - +
513A GLU* 1.3 60.1 + - + +
515A ALA* 3.5 8.3 - - - +
516A TRP* 2.8 31.2 + - - +
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Residues in contact with GLU 513 (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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511A SER* 3.2 10.2 + - - +
512A LYS* 1.3 76.6 - - + +
514A VAL* 1.3 65.0 + - + +
516A TRP* 3.5 8.0 + - - +
517A ASN* 3.3 19.8 + - - +
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Residues in contact with VAL 514 (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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509A ARG* 4.3 15.9 - - + -
511A SER* 3.2 27.4 + - - +
513A GLU* 1.3 74.9 - - + +
515A ALA* 1.3 66.4 + - - +
517A ASN* 3.2 9.4 + - + +
518A LEU* 3.0 41.5 + - + +
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Residues in contact with ALA 515 (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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502A LEU* 3.5 5.5 - - + +
505A HIS* 3.8 14.0 + - + -
506A VAL* 3.4 44.0 - - + +
509A ARG* 5.8 0.6 - - - +
511A SER 2.9 18.2 + - - +
512A LYS 3.5 3.4 - - - +
514A VAL* 1.3 78.4 - - - +
516A TRP* 1.3 60.7 + - - +
518A LEU* 3.2 5.2 + - - +
519A THR* 2.8 28.2 + - - +
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Residues in contact with TRP 516 (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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429A LEU* 3.5 29.6 - - + +
432A ALA* 3.7 5.6 - - + -
433A ARG* 3.3 83.1 - - + +
436A MET* 3.9 19.3 - - + -
502A LEU* 3.6 22.6 - - + +
512A LYS 2.8 17.4 + - - +
513A GLU* 3.6 9.2 - - - +
514A VAL 3.2 0.2 - - - -
515A ALA* 1.3 76.1 - - - +
517A ASN* 1.3 64.6 + - - +
519A THR* 3.2 3.6 + - - -
520A SER* 2.9 24.2 + - - -
523A LEU* 3.4 30.9 - - + +
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Residues in contact with ASN 517 (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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513A GLU 3.3 10.2 + - - +
514A VAL* 3.2 11.2 + - - +
516A TRP* 1.3 82.8 - - - +
518A LEU* 1.3 75.5 + - - +
520A SER* 2.6 34.2 + - - -
699A FAD 6.2 0.3 - - - -
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Residues in contact with LEU 518 (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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505A HIS* 3.4 31.1 - - + +
509A ARG* 3.3 48.5 - - - +
514A VAL* 3.0 29.1 + - + +
515A ALA 3.2 1.8 + - - +
517A ASN* 1.3 87.6 - - - +
519A THR* 1.3 56.7 - - - +
521A VAL 5.4 0.8 + - - -
522A ASP* 5.3 1.0 - - - +
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Residues in contact with THR 519 (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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498A ALA 4.5 3.6 - - - -
501A ASN* 3.2 12.8 - - + -
502A LEU* 3.1 46.1 - - - +
505A HIS* 2.9 34.5 - - + +
515A ALA 2.8 12.5 + - - -
516A TRP* 3.4 3.7 + - - -
517A ASN 3.1 0.4 - - - -
518A LEU* 1.3 74.4 - - - +
520A SER* 1.3 59.7 + - - +
521A VAL 3.3 2.9 - - - -
522A ASP* 3.1 13.2 + - - +
523A LEU* 2.8 31.6 + - - +
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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