Contacts of the helix formed by residues 510 - 519 (chain A) in PDB entry 1JEQ
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 LYS 510 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A LEU* 5.5 7.2 - - - +
508A LEU 4.5 7.6 - - - +
509A PRO* 1.3 66.6 - - - +
511A VAL* 1.3 60.5 + - - +
512A GLU 3.7 1.1 - - - -
513A ALA* 3.4 17.8 + - + -
514A MET* 2.9 36.1 + - + +
343B LEU 5.8 0.6 + - - -
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Residues in contact with VAL 511 (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 PRO* 2.7 29.5 + - + +
510A LYS* 1.3 67.6 - - - +
512A GLU* 1.3 80.0 + - - +
513A ALA 3.0 0.7 + - - -
514A MET* 3.1 7.5 + - - +
515A ASN* 2.8 34.9 + - - +
254B GLY* 4.6 9.0 - - - +
255B SER* 3.3 38.6 - - - +
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Residues in contact with GLU 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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510A LYS 3.7 0.2 - - - -
511A VAL* 1.3 87.7 - - + +
513A ALA* 1.3 62.1 + - - +
515A ASN* 3.3 13.6 + - - +
516A LYS* 3.0 24.8 + - - +
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Residues in contact with ALA 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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510A LYS* 3.4 24.1 + - + +
511A VAL 3.0 1.2 + - - -
512A GLU* 1.3 76.6 - - - +
514A MET* 1.3 68.4 + - + +
516A LYS* 2.9 8.3 + - - +
517A ARG* 2.8 25.7 + - - +
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Residues in contact with MET 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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469A LEU* 4.0 28.0 - - + -
509A PRO* 4.0 17.3 - - - -
510A LYS* 2.9 30.7 + - + +
511A VAL* 3.6 3.4 - - - +
513A ALA* 1.3 71.3 - - + +
515A ASN* 1.3 64.8 + - - +
517A ARG* 3.2 3.9 + - - +
518A LEU* 2.9 31.9 + - + +
253B ILE* 4.1 15.0 - - + -
254B GLY* 3.3 33.9 - - - +
342B VAL* 3.3 30.1 - - + +
343B LEU 4.3 14.8 - - - +
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Residues in contact with ASN 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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511A VAL* 2.8 27.9 + - - +
512A GLU* 3.3 19.7 + - - +
514A MET* 1.3 69.5 - - - +
516A LYS* 1.3 65.7 + - - +
518A LEU* 2.9 19.5 + - - +
519A GLY* 3.2 11.1 + - - +
522A VAL* 6.4 0.9 - - - -
254B GLY* 3.5 5.5 - - - -
255B SER* 3.0 43.4 + - - -
256B ASN* 3.7 18.5 + - - +
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Residues in contact with LYS 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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512A GLU 3.0 9.7 + - - +
513A ALA* 2.9 9.4 + - - +
515A ASN* 1.3 78.8 - - - +
517A ARG* 1.3 64.5 + - - +
518A LEU 3.1 1.0 + - - -
519A GLY* 3.2 11.7 + - - -
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Residues in contact with ARG 517 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A GLU 4.3 2.8 + - - -
468A LYS* 2.6 75.2 + - + +
469A LEU* 5.0 3.1 - - + -
513A ALA 2.8 21.3 + - - +
514A MET* 3.8 6.7 - - - +
516A LYS* 1.3 74.0 - - - +
518A LEU* 1.3 60.8 + - - +
519A GLY 3.4 0.2 - - - -
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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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465A ILE* 3.4 40.8 - - + +
468A LYS* 4.1 7.6 - - + -
469A LEU* 4.0 27.4 - - + -
514A MET* 2.9 26.4 + - + +
515A ASN* 2.9 8.9 + - - +
517A ARG* 1.3 76.3 - - - +
519A GLY* 1.3 68.1 + - - +
520A SER 3.4 0.2 + - - -
521A LEU* 3.2 31.1 + - + +
522A VAL* 3.9 26.2 - - + -
253B ILE* 4.3 18.2 - - + +
254B GLY* 5.1 1.3 - - - -
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Residues in contact with GLY 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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515A ASN 3.2 7.2 + - - +
516A LYS 3.2 14.5 + - - -
517A ARG 3.4 0.6 - - - -
518A LEU* 1.3 80.5 - - - +
520A SER* 1.3 62.2 + - - -
522A VAL* 4.1 9.5 + - - +
523A ASP 5.2 0.2 + - - -
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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