Contacts of the helix formed by residues 551 - 562 (chain A) in PDB entry 2JGN
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 ILE 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517A LEU* 4.8 10.1 - - + -
518A PRO* 3.6 28.0 - - + +
519A SER 4.5 3.1 - - - +
520A ASP* 3.5 31.6 - - - +
521A ILE* 3.6 30.5 - - + +
524A TYR* 4.5 3.4 - - + -
544A PHE* 4.0 14.8 - - + -
548A ASN* 3.0 23.8 + - + +
550A ASN* 1.3 82.3 - - - +
552A THR* 1.3 64.7 + - - +
553A LYS 3.5 2.0 - - - -
554A ASP* 3.4 10.4 + - + +
555A LEU* 2.9 27.3 + - + +
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Residues in contact with THR 552 (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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544A PHE* 3.5 18.8 - - + -
548A ASN 3.5 1.2 + - - -
549A ILE* 2.8 45.0 + - - +
550A ASN 3.4 0.4 - - - -
551A ILE* 1.3 77.5 - - - +
553A LYS* 1.3 62.2 + - - +
555A LEU* 3.4 2.1 + - - +
556A LEU* 3.0 27.0 + - - +
570A LEU* 3.8 20.3 - - + +
573A MET* 3.9 10.4 - - + +
574A ALA* 3.5 33.7 - - + +
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Residues in contact with LYS 553 (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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549A ILE 5.9 0.2 - - - +
550A ASN 5.2 1.9 + - - -
551A ILE 3.5 0.6 - - - -
552A THR* 1.3 75.6 - - - +
554A ASP* 1.3 66.9 + - - +
556A LEU* 3.3 3.3 + - - +
557A ASP* 2.9 37.8 + - - +
574A ALA* 4.2 33.2 - - + +
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Residues in contact with ASP 554 (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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520A ASP* 5.9 0.7 - - - -
521A ILE* 3.8 36.0 + - + +
550A ASN 4.9 7.1 - - - +
551A ILE* 3.4 12.6 + - + +
553A LYS* 1.3 82.2 - - - +
555A LEU* 1.3 63.6 + - - +
557A ASP* 3.3 8.7 + - - +
558A LEU* 3.0 24.4 + - - +
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Residues in contact with LEU 555 (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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418A VAL* 4.0 24.0 - - + -
517A LEU* 4.3 13.5 - - + -
521A ILE* 3.7 14.2 - - + +
524A TYR* 3.9 34.8 - - + +
544A PHE* 3.8 31.6 - - + -
551A ILE* 2.9 23.3 + - + +
552A THR* 3.8 3.6 - - - +
554A ASP* 1.3 75.1 - - - +
556A LEU* 1.3 63.2 + - - +
558A LEU* 3.3 2.4 + - + +
559A LEU* 2.9 44.5 + - + +
570A LEU* 4.4 5.8 - - + -
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Residues in contact with LEU 556 (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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552A THR 3.0 18.0 + - - +
553A LYS* 3.6 6.5 - - - +
554A ASP 3.3 0.2 - - - -
555A LEU* 1.3 75.5 - - - +
557A ASP* 1.3 69.3 + - - +
559A LEU* 3.1 3.8 + - - -
560A VAL* 3.0 38.7 + - + +
566A VAL* 3.3 35.7 - - + -
570A LEU* 4.1 18.7 - - + +
571A GLU* 4.1 22.4 - - + +
574A ALA* 3.6 25.1 - - + -
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Residues in contact with ASP 557 (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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553A LYS* 2.9 25.6 + - - +
554A ASP* 3.9 8.7 - - - +
556A LEU* 1.3 84.0 - - - +
558A LEU* 1.3 58.9 + - - +
560A VAL* 3.4 7.1 + - - +
561A GLU* 3.0 33.4 + - - +
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Residues in contact with LEU 558 (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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411A SER* 3.8 15.9 - - - +
416A GLN* 3.3 28.0 - - - +
521A ILE* 3.5 31.9 - - + -
524A TYR* 3.7 18.2 - - + -
525A VAL* 3.8 18.4 - - + -
528A ILE* 5.1 0.9 - - + -
554A ASP 3.0 16.3 + - - +
555A LEU* 3.6 4.9 - - + +
557A ASP* 1.3 77.6 - - - +
559A LEU* 1.3 67.0 + - + +
561A GLU* 3.3 20.0 + - - +
562A ALA* 3.0 26.3 + - - +
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Residues in contact with LEU 559 (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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416A GLN* 3.7 36.6 - - + +
418A VAL* 3.7 25.6 - - + -
524A TYR* 4.5 1.8 - - - +
555A LEU* 2.9 22.0 + - + +
556A LEU 3.7 3.4 - - - +
558A LEU* 1.3 77.3 - - + +
560A VAL* 1.3 60.9 + - - +
562A ALA 3.4 0.5 + - - -
563A LYS 3.2 3.1 + - - -
564A GLN* 2.7 51.0 + - + +
565A GLU 3.8 13.5 - - - +
566A VAL* 3.9 14.1 - - + -
567A PRO* 4.6 1.1 - - + -
570A LEU* 3.6 30.5 - - + -
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Residues in contact with VAL 560 (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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556A LEU* 3.0 36.2 + - + +
557A ASP* 3.7 7.6 - - - +
559A LEU* 1.3 77.5 - - - +
561A GLU* 1.3 62.2 + - - +
563A LYS* 3.0 18.1 + - - +
564A GLN 5.3 0.7 - - - -
566A VAL* 4.2 10.1 - - + -
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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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410A THR* 4.3 23.7 + - + +
412A GLU* 3.7 5.1 - - - +
557A ASP* 3.0 22.9 + - - +
558A LEU* 3.4 21.4 - - + +
560A VAL* 1.3 78.5 - - - +
562A ALA* 1.3 56.4 + - - +
563A LYS* 3.1 24.1 + - - +
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Residues in contact with ALA 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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410A THR* 4.5 5.6 - - + -
411A SER* 3.8 21.5 - - - +
412A GLU* 3.7 29.4 - - - +
416A GLN* 4.4 0.9 - - - +
558A LEU* 3.0 18.1 + - + +
560A VAL 3.2 0.2 - - - -
561A GLU* 1.3 75.1 - - - +
563A LYS* 1.3 70.0 + - - +
564A GLN* 3.0 30.5 - - + +
569C TRP* 4.1 2.3 - - - +
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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