Contacts of the helix formed by residues 524 - 529 (chain B) in PDB entry 1M7X
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 524 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLU* 3.2 15.9 - - - -
481B TRP* 3.4 35.7 - - - -
522B PRO* 3.5 3.4 - - - -
523B LEU* 1.3 80.9 - - - +
525B HIS* 1.3 64.2 + - - +
526B ASP* 3.2 21.7 + - - +
527B GLU* 3.4 24.5 + - - +
528B VAL* 4.0 9.4 - - - +
565B LEU* 4.1 4.5 - - - -
567B PHE* 3.8 3.2 - - - +
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Residues in contact with HIS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLU* 2.6 32.5 + - - -
287B LEU* 3.9 10.3 - - + +
298B TRP* 3.7 29.8 - + - -
300B TYR* 3.3 31.0 + + - -
403B ARG* 4.6 5.9 + - - -
481B TRP* 5.0 0.2 - + - -
524B SER* 1.3 76.8 - - - +
526B ASP* 1.3 89.5 + - - +
527B GLU 3.1 3.0 + - - -
528B VAL* 3.4 11.4 + - - +
529B VAL* 3.4 19.8 - - - +
567B PHE* 3.5 39.7 - - + -
578B TRP* 3.8 7.5 - - + -
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Residues in contact with ASP 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B TRP* 4.0 10.2 - - - -
403B ARG* 5.0 3.5 + - - -
458B GLU* 5.6 2.9 - - - +
481B TRP* 5.0 6.6 - - - -
524B SER* 3.2 10.2 + - - +
525B HIS* 1.3 103.0 + - - +
527B GLU* 1.3 73.0 + - - +
528B VAL 3.3 0.2 - - - -
529B VAL* 3.4 19.1 - - - +
532B LYS* 3.5 18.6 + - - +
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Residues in contact with GLU 527 (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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483B LEU* 5.2 3.1 - - - +
486B MET* 3.4 48.4 - - + +
487B HIS* 4.8 4.0 + - - -
490B LEU* 4.8 3.8 - - + -
523B LEU* 5.1 1.6 - - - -
524B SER* 3.4 23.1 + - - +
525B HIS 3.1 1.2 - - - -
526B ASP* 1.3 94.8 - - - +
528B VAL* 1.3 54.3 + - + +
529B VAL 3.6 1.6 - - - -
532B LYS* 3.5 28.5 + - - +
533B LYS 3.3 0.7 - - - +
535B ILE* 4.8 4.5 - - + -
538B ARG* 2.3 48.8 + - - +
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Residues in contact with VAL 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B SER 4.0 4.7 - - - +
525B HIS* 3.5 15.9 - - - +
526B ASP 3.3 0.4 - - - -
527B GLU* 1.3 85.2 - - - +
529B VAL* 1.3 58.3 - - - +
533B LYS 3.5 15.0 - - - +
534B SER* 4.0 12.1 - - - -
535B ILE* 4.0 25.8 - - + -
567B PHE* 3.9 26.0 - - + -
570B ASN* 4.1 10.5 - - - +
577B GLU* 2.8 24.9 - - - +
578B TRP* 2.9 24.4 + - + +
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Residues in contact with VAL 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B TRP* 3.9 17.5 - - + -
525B HIS 3.4 7.4 - - - +
526B ASP* 3.4 22.2 - - - +
527B GLU 3.6 0.2 - - - -
528B VAL* 1.3 82.6 - - - +
530B HIS* 1.3 90.3 + - + +
532B LYS* 2.9 28.7 + - + +
577B GLU* 3.1 10.3 - - - -
578B TRP* 3.4 42.2 - - + +
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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