Contacts of the helix formed by residues 560 - 570 (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 SER 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A TYR* 1.3 75.7 + - - +
561A GLU* 1.3 68.9 + - - +
562A GLU* 2.9 16.0 + - - -
563A GLU* 2.9 22.7 + - - +
564A LEU* 3.2 9.4 + - - +
588A TYR* 4.0 1.3 - - - -
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Residues in contact with GLU 561 (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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560A SER* 1.3 71.4 - - - +
562A GLU* 1.3 65.4 + - + +
564A LEU 3.5 0.3 + - - -
565A LYS* 2.9 27.1 + - - +
588A TYR* 3.0 31.4 + - + +
606A HIS* 5.9 1.2 - - - -
607A PHE* 3.7 18.1 - - + -
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Residues in contact with GLU 562 (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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560A SER* 2.9 11.7 + - - -
561A GLU* 1.3 76.7 - - + +
563A GLU* 1.3 65.3 + - - +
565A LYS* 2.9 17.2 + - - +
566A THR* 2.8 18.6 + - - +
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Residues in contact with GLU 563 (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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559A TYR* 3.5 36.5 + - - -
560A SER* 2.9 18.2 + - - +
562A GLU* 1.3 74.9 - - - +
564A LEU* 1.3 56.6 + - - +
566A THR* 2.8 25.4 + - - -
567A HIS* 2.9 43.1 + - + +
576A PHE* 4.7 0.3 - - - -
155B LYS* 3.4 17.4 + - - -
213B ILE* 4.0 8.2 - - - +
214B SER* 3.3 30.6 + - - +
217B GLY* 5.7 3.8 - - - -
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Residues in contact with LEU 564 (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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559A TYR* 3.1 47.6 - - + +
560A SER 3.2 2.0 + - - +
561A GLU 4.0 5.6 - - - +
563A GLU* 1.3 80.2 - - + +
565A LYS* 1.3 61.6 + - - +
567A HIS* 3.4 7.4 + - + +
568A ILE* 3.1 32.1 + - + +
573A LEU* 3.9 24.7 - - + -
576A PHE* 4.1 18.4 - - + -
584A ALA* 4.7 12.1 - - + -
588A TYR* 3.8 20.0 - - + +
603A LEU* 4.9 5.4 - - + -
607A PHE* 3.9 21.5 - - + -
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Residues in contact with LYS 565 (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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561A GLU 2.9 21.1 + - - +
562A GLU* 2.9 7.4 + - - +
564A LEU* 1.3 76.7 - - - +
566A THR* 1.3 61.0 + - - +
568A ILE* 3.6 10.8 + - + +
569A SER* 3.2 21.1 + - - -
607A PHE* 4.5 14.5 - - + -
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Residues in contact with THR 566 (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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562A GLU* 2.8 16.5 + - - +
563A GLU* 2.8 11.5 + - - -
565A LYS* 1.3 75.0 - - - +
567A HIS* 1.3 58.6 + - - +
568A ILE 3.1 1.6 - - - -
569A SER* 3.1 6.8 + - - +
570A LYS* 2.8 46.9 + - + +
213B ILE* 4.2 14.4 - - + -
217B GLY* 5.2 2.0 - - - -
218B GLU* 4.1 38.4 + - + +
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Residues in contact with HIS 567 (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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563A GLU* 2.9 47.8 + - + +
564A LEU* 3.7 9.6 - - + +
566A THR* 1.3 75.6 - - - +
568A ILE* 1.3 58.2 + - - +
570A LYS* 3.4 0.8 + - - -
571A GLY* 2.8 8.8 + - - -
572A THR* 2.7 51.7 + - - +
573A LEU* 3.4 21.2 + - + +
576A PHE* 3.7 26.6 - + - -
210B MET* 3.7 12.3 - - + -
213B ILE* 3.3 21.9 - - + +
214B SER* 3.0 28.9 + - - -
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Residues in contact with ILE 568 (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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564A LEU* 3.1 18.8 + - + +
565A LYS* 3.7 10.5 - - + +
566A THR 3.1 0.6 - - - -
567A HIS* 1.3 74.5 - - - +
569A SER* 1.3 64.9 + - - +
571A GLY* 3.3 11.9 + - - +
573A LEU* 3.7 27.4 - - + -
603A LEU 4.3 6.1 - - - +
604A THR* 3.9 41.5 - - + +
607A PHE* 4.4 17.5 - - + -
608A GLN* 5.5 7.4 - - + +
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Residues in contact with SER 569 (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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565A LYS 3.2 11.8 + - - -
566A THR* 3.1 12.0 + - - -
568A ILE* 1.3 81.5 - - - +
570A LYS* 1.3 71.2 + - - +
571A GLY 3.6 0.3 + - - -
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Residues in contact with LYS 570 (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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566A THR* 2.8 26.5 + - + +
567A HIS 4.2 0.7 - - - +
569A SER* 1.3 87.4 - - - +
571A GLY* 1.3 64.2 + - - +
572A THR* 3.3 10.7 + - + +
206B GLU* 4.9 1.0 - - - +
209B LYS* 4.6 11.8 + - - +
213B ILE* 3.8 28.3 - - + -
218B GLU* 4.7 18.5 - - - +
221B LEU* 4.0 23.5 - - + +
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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