Contacts of the helix formed by residues 560 - 566 (chain B) in PDB entry 5M64
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 ARG 560 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558B VAL* 2.9 23.2 - - + +
559B SER* 1.3 82.1 - - - +
561B ILE* 1.3 66.9 + - - +
562B PRO 3.4 2.5 - - - -
563B SER* 3.5 16.2 - - - +
564B ILE* 3.0 38.8 + - + +
618B PRO* 3.4 39.4 + - - +
619B GLY* 3.4 26.8 - - - +
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Residues in contact with ILE 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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558B VAL* 3.6 24.8 - - + +
560B ARG* 1.3 76.4 - - - +
562B PRO* 1.3 63.8 - - + +
564B ILE* 3.3 8.5 - - + +
565B LEU* 2.9 28.0 + - + +
588B ILE* 4.0 31.0 - - + -
619B GLY 4.1 0.4 - - - +
620B LEU* 3.8 27.4 - - + -
621B PRO* 4.4 9.2 - - + -
624B LEU* 4.4 22.0 - - + -
642B LEU* 4.0 22.2 - - + -
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Residues in contact with PRO 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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559B SER* 4.7 6.7 - - - +
560B ARG* 3.7 4.0 - - - +
561B ILE* 1.3 92.7 - - + +
563B SER* 1.3 64.1 + - - +
564B ILE 3.0 2.5 - - - -
565B LEU* 2.8 25.5 + - + -
566B TYR* 3.0 38.2 + - + +
588B ILE* 4.1 10.3 - - + -
593B ILE* 4.0 21.8 - - + -
70M SER* 6.3 0.9 - - - -
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Residues in contact with SER 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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559B SER 3.6 16.5 + - - -
560B ARG* 3.1 22.3 + - - +
562B PRO* 1.3 80.2 - - - +
564B ILE* 1.3 62.1 + - - +
566B TYR* 3.6 22.0 + - - -
567B SER* 3.2 18.7 - - - -
73M SER* 5.0 6.1 + - - -
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Residues in contact with ILE 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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560B ARG* 3.0 33.0 + - + +
561B ILE* 3.3 14.6 - - + +
563B SER* 1.3 79.4 - - - +
565B LEU* 1.3 64.7 + - + +
567B SER* 3.0 19.9 + - - +
568B LEU* 3.2 20.6 + - + +
608B LEU* 4.3 19.7 - - + -
611B TRP* 6.5 1.3 - - + -
619B GLY* 5.0 4.0 - - - +
620B LEU* 3.7 35.0 - - + -
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Residues in contact with LEU 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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561B ILE* 2.9 19.4 + - + +
562B PRO* 2.8 8.8 + - + +
564B ILE* 1.3 76.0 - - + +
566B TYR* 1.3 64.0 + - - +
567B SER 3.1 0.9 - - - -
568B LEU* 3.0 17.9 + - + +
570B VAL* 3.2 37.3 + - + +
586B VAL* 3.6 21.3 - - + -
588B ILE* 4.5 7.6 - - + -
593B ILE* 3.6 35.0 - - + -
604B ILE* 4.9 8.5 - - + -
608B LEU* 4.6 24.5 - - + -
642B LEU* 4.0 14.6 - - + -
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Residues in contact with TYR 566 (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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562B PRO* 3.0 40.3 - - + +
563B SER* 3.6 24.0 + - - -
565B LEU* 1.3 79.1 - - + +
567B SER* 1.3 65.9 + - - +
568B LEU 3.3 0.2 - - - -
569B GLY* 3.4 9.6 + - - -
570B VAL* 3.3 31.9 + - + +
571B ALA 5.1 4.0 - - - +
572B PRO* 5.3 5.6 - - + -
593B ILE* 5.3 8.7 - - + +
70M SER* 2.5 26.9 + - - -
73M SER* 2.4 47.1 + - - -
74M ASN* 4.8 11.7 - - + -
57N LYS* 4.1 13.7 + - - +
58N PHE 5.8 1.0 - - - -
59N PRO* 5.5 2.0 - - + +
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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