Contacts of the helix formed by residues 554 - 565 (chain A) in PDB entry 5M7R
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 THR 554 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A LEU* 3.8 5.8 - - - -
552A PRO* 3.7 17.7 - - + +
553A VAL* 1.3 80.1 - - - +
555A LEU* 1.3 63.2 + - - +
556A GLU* 3.4 18.9 + - - +
557A ASP* 3.0 44.0 + - - +
558A LEU* 3.5 7.1 + - - +
627A ARG* 4.8 6.4 + - - +
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Residues in contact with LEU 555 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A LYS* 5.2 7.2 - - + +
384A LEU* 4.1 17.0 - - + +
385A THR* 3.4 49.6 - - + +
388A LEU* 3.6 22.3 - - + +
554A THR* 1.3 72.7 - - - +
556A GLU* 1.3 75.1 + - - +
558A LEU* 3.2 5.4 + - + +
559A GLN* 3.0 39.5 + - + +
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Residues in contact with GLU 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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554A THR* 3.2 19.6 - - - +
555A LEU* 1.3 90.8 + - - +
557A ASP* 1.3 62.7 + - - +
559A GLN* 3.5 17.6 + - - +
560A LEU* 3.1 24.1 + - - +
574A LYS* 4.9 9.2 + - - +
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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 VAL* 3.8 10.8 - - + +
554A THR* 3.0 37.1 + - - +
555A LEU 3.2 0.2 - - - -
556A GLU* 1.3 76.2 - - - +
558A LEU* 1.3 61.6 + - + +
560A LEU* 3.6 4.2 + - - +
561A LEU* 2.9 24.1 + - - +
620A LEU 4.9 1.0 - - - +
624A MET* 3.4 35.3 - - + +
627A ARG* 2.7 47.3 + - - +
628A LEU* 5.8 1.6 - - + -
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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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384A LEU* 4.1 24.9 - - + +
387A TRP* 4.4 11.7 - - + -
388A LEU* 3.8 33.2 - - + +
391A PHE* 3.8 40.8 - - + -
553A VAL* 4.0 14.6 - - + -
554A THR 3.5 10.3 + - - +
555A LEU* 3.2 7.9 + - - +
557A ASP* 1.3 76.7 - - + +
559A GLN* 1.3 67.3 + - - +
561A LEU* 3.8 18.5 - - + +
562A ALA* 3.0 26.3 + - - +
628A LEU* 4.5 4.3 - - + -
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Residues in contact with GLN 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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380A LEU* 5.8 1.9 - - + +
381A LYS* 3.9 33.6 - - + +
384A LEU* 3.9 22.4 - - + +
555A LEU* 3.0 33.4 + - + +
556A GLU* 3.7 28.5 - - - +
558A LEU* 1.3 77.3 - - - +
560A LEU* 1.3 56.2 + - - +
562A ALA* 3.6 1.9 + - - +
563A ASP* 3.1 36.5 + - - +
574A LYS* 4.6 16.5 + - - +
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Residues in contact with LEU 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 GLU 3.1 17.7 + - - +
557A ASP* 3.7 6.1 - - - +
559A GLN* 1.3 74.1 - - - +
561A LEU* 1.3 67.1 + - - +
563A ASP* 3.0 13.8 + - - -
564A LEU* 3.1 33.1 + - + +
574A LYS* 4.2 28.9 - - + +
578A MET* 4.0 22.9 - - + -
620A LEU* 3.5 44.4 - - + +
621A VAL* 4.1 8.1 - - + +
624A MET* 4.3 9.0 - - + -
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Residues in contact with LEU 561 (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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293A LEU* 3.8 11.9 - - + -
387A TRP* 5.0 4.9 - - + -
391A PHE* 5.8 0.4 - - + -
557A ASP 2.9 22.1 + - - +
558A LEU* 3.3 18.6 + - + +
560A LEU* 1.3 72.8 - - - +
562A ALA* 1.3 62.5 + - - +
564A LEU* 3.2 5.6 + - - +
565A PHE* 3.1 39.5 + - + +
624A MET* 3.7 30.5 - - + +
628A LEU* 4.2 17.9 - - + -
640A MET* 3.8 26.2 - - + -
644A VAL* 3.7 20.4 - - + -
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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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293A LEU* 3.9 35.4 - - + +
380A LEU* 4.6 5.6 - - + -
384A LEU* 4.5 18.2 - - + -
387A TRP* 6.3 0.2 - - + -
558A LEU 3.0 17.2 + - - +
559A GLN 3.9 4.0 - - - +
561A LEU* 1.3 77.5 - - - +
563A ASP* 1.3 66.2 + - - +
565A PHE 3.0 21.0 - - - +
566A TYR* 3.1 12.6 - - + +
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Residues in contact with ASP 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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380A LEU* 4.5 8.5 - - - +
559A GLN* 3.1 20.7 + - - +
560A LEU* 3.0 7.7 + - + +
562A ALA* 1.3 77.0 - - - +
564A LEU* 1.3 58.0 + - - +
565A PHE 3.8 0.2 + - - -
566A TYR* 3.8 11.6 - - - +
571A HIS* 3.9 4.9 - - - +
572A GLY* 2.9 35.1 + - - +
573A PRO* 3.4 27.1 - - - +
574A LYS* 3.0 45.2 + - + +
575A GLY* 4.0 6.0 + - - +
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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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560A LEU* 3.1 24.1 + - + +
561A LEU* 3.6 6.5 - - + +
562A ALA 3.2 0.2 - - - -
563A ASP* 1.3 77.9 - - - +
565A PHE* 1.3 74.1 + - + +
566A TYR* 3.8 1.3 + - - -
571A HIS* 5.0 3.1 + - - -
575A GLY* 4.3 11.0 - - - -
578A MET* 4.9 2.9 - - + -
621A VAL* 4.1 15.5 - - + -
624A MET* 3.3 33.4 - - + -
647A ILE* 4.0 27.0 - - + +
651A MET* 4.6 9.9 - - + -
685B LEU* 3.6 46.6 + - + +
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Residues in contact with PHE 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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289A LYS 4.1 17.5 - - - -
290A ARG* 5.1 0.9 - - - -
291A LEU* 3.2 43.3 - - + +
293A LEU* 2.7 39.8 + - + +
561A LEU* 3.1 33.2 + - + +
562A ALA 3.0 6.4 - - - +
564A LEU* 1.3 85.2 - - + +
566A TYR* 1.3 53.0 + - - +
643A TYR* 3.3 44.2 - - + -
646A ASP* 5.7 2.2 - - + -
647A ILE* 4.0 31.4 - - + -
685B LEU 6.1 2.2 - - - -
686B ALA* 5.8 6.3 - - + -
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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