Contacts of the helix formed by residues 554 - 565 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388B LEU* 3.8 6.5 - - - -
552B PRO* 3.7 17.3 - - + +
553B VAL* 1.3 79.0 - - - +
555B LEU* 1.3 62.9 + - - +
556B GLU* 3.4 19.0 + - - +
557B ASP* 3.0 41.7 + - - +
558B LEU* 3.5 10.0 + - - +
627B ARG* 4.8 4.9 - - - +
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Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B LYS* 4.9 17.0 - - + +
384B LEU* 4.1 17.0 - - + +
385B THR* 4.0 41.3 - - + +
388B LEU* 3.6 22.7 - - + +
554B THR* 1.3 70.7 - - - +
556B GLU* 1.3 78.2 + - - +
558B LEU* 3.1 4.8 + - + +
559B GLN* 3.0 38.2 + - + +
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Residues in contact with GLU 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B THR* 3.2 20.7 - - - +
555B LEU* 1.3 92.2 + - - +
557B ASP* 1.3 62.6 + - - +
559B GLN* 3.5 17.5 + - - +
560B LEU* 3.1 24.6 + - - +
574B LYS* 4.9 6.8 + - - +
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Residues in contact with ASP 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B VAL* 3.8 11.1 - - + -
554B THR* 3.0 38.8 + - - +
555B LEU 3.2 0.2 - - - -
556B GLU* 1.3 78.9 - - - +
558B LEU* 1.3 58.0 + - + +
560B LEU* 3.6 4.3 + - - +
561B LEU* 2.9 23.6 + - - +
620B LEU 4.9 1.2 - - - +
624B MET* 3.4 34.7 - - + +
627B ARG* 2.8 48.4 + - - +
628B LEU* 6.0 1.1 - - + -
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Residues in contact with LEU 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B LEU* 4.0 26.1 - - + +
387B TRP* 4.3 11.5 - - + -
388B LEU* 3.8 33.4 - - + +
391B PHE* 3.8 41.1 - - + -
553B VAL* 4.0 13.7 - - + -
554B THR 3.5 9.2 + - - +
555B LEU* 3.1 9.2 + - - +
557B ASP* 1.3 76.6 - - + +
559B GLN* 1.3 65.6 + - - +
561B LEU* 3.8 19.3 - - + +
562B ALA* 3.0 26.0 + - - +
628B LEU* 4.7 4.3 - - + -
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Residues in contact with GLN 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LEU* 5.9 1.5 - - + +
381B LYS* 4.0 32.3 - - + +
384B LEU* 3.9 22.0 - - + -
555B LEU* 3.0 28.0 + - + +
556B GLU* 3.7 27.2 - - - +
558B LEU* 1.3 76.9 - - - +
560B LEU* 1.3 56.3 + - - +
562B ALA* 3.9 1.7 - - - +
563B ASP* 3.1 36.0 + - - +
574B LYS* 4.4 16.9 + - - +
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Residues in contact with LEU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B GLU 3.1 17.3 + - - +
557B ASP* 3.7 5.8 - - - +
559B GLN* 1.3 74.7 - - - +
561B LEU* 1.3 67.2 + - - +
563B ASP* 3.0 13.2 + - - +
564B LEU* 3.1 32.1 + - + +
574B LYS* 4.2 28.1 - - + +
578B MET* 4.0 24.0 - - + -
617B MET* 5.4 3.1 - - + -
620B LEU* 3.6 43.7 - - + +
621B VAL* 4.0 9.2 - - + +
624B MET* 4.4 8.7 - - + -
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Residues in contact with LEU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B LEU* 3.8 11.8 - - + +
387B TRP* 4.9 4.5 - - + -
391B PHE* 5.8 0.2 - - + -
557B ASP 2.9 21.8 + - - +
558B LEU* 3.3 19.3 + - + +
560B LEU* 1.3 73.1 - - - +
562B ALA* 1.3 61.6 + - - +
564B LEU* 3.2 5.6 + - - +
565B PHE* 3.1 38.7 + - + +
624B MET* 3.7 25.5 - - + +
628B LEU* 4.2 18.2 - - + -
640B MET* 3.8 26.0 - - + -
644B VAL* 3.3 28.7 - - + -
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Residues in contact with ALA 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B LEU* 3.9 36.5 - - + +
380B LEU* 4.5 6.1 - - + -
384B LEU* 4.5 17.3 - - + -
558B LEU 3.0 17.9 + - - +
559B GLN 3.9 4.0 - - - +
561B LEU* 1.3 74.2 - - - +
563B ASP* 1.3 68.8 + - - +
565B PHE 3.0 20.4 - - - -
566B TYR* 3.1 13.7 - - + +
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Residues in contact with ASP 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LEU* 4.6 7.4 - - - +
559B GLN* 3.1 20.5 + - - +
560B LEU* 3.0 6.5 + - + +
562B ALA* 1.3 78.1 - - - +
564B LEU* 1.3 58.7 + - - +
566B TYR* 3.8 11.8 - - - +
571B HIS* 3.9 4.9 - - - +
572B GLY* 2.9 35.8 + - - +
573B PRO* 3.4 26.7 - - - +
574B LYS* 3.0 43.6 + - + +
575B GLY* 4.1 5.6 + - - +
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Residues in contact with LEU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A LEU* 3.4 48.2 + - + +
560B LEU* 3.1 23.7 + - + +
561B LEU* 3.6 6.3 - - - +
562B ALA 3.2 0.2 - - - -
563B ASP* 1.3 78.4 - - - +
565B PHE* 1.3 74.7 + - + +
566B TYR 3.8 1.1 + - - -
571B HIS* 4.8 3.7 + - - -
575B GLY* 4.2 11.9 - - - -
578B MET* 4.8 3.8 - - + -
621B VAL* 4.1 15.3 - - + -
624B MET* 3.4 33.7 - - + -
647B ILE* 4.1 19.8 - - + +
651B MET* 4.6 11.7 - - + -
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Residues in contact with PHE 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A GLN* 5.9 0.2 - - - -
685A LEU* 6.1 2.2 - - + -
686A ALA* 5.9 6.5 - - + -
289B LYS 4.1 17.3 - - - -
290B ARG* 5.1 1.1 - - - -
291B LEU* 3.2 42.2 - - + +
293B LEU* 2.7 38.7 + - + +
561B LEU* 3.1 33.6 + - + +
562B ALA 3.0 6.6 - - - +
564B LEU* 1.3 85.8 - - + +
566B TYR* 1.3 54.6 + - - +
643B TYR* 3.4 44.2 - + + -
646B ASP* 5.7 1.1 - - + -
647B ILE* 4.0 30.1 - - + -
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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