Contacts of the helix formed by residues 523 - 531 (chain B) in PDB entry 3RMD
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 523 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521B ASP 3.2 6.2 + - - -
522B PHE* 1.3 71.0 - - - +
524B ASP* 1.3 62.4 + - - +
525B GLU* 3.7 3.0 + - - +
526B ILE* 3.0 22.3 + - - +
527B LYS* 2.7 45.5 + - - +
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Residues in contact with ASP 524 (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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523B SER* 1.3 76.1 + - - +
525B GLU* 1.3 54.8 + - - +
526B ILE 2.5 17.4 + - - -
527B LYS* 3.0 37.6 + - - +
528B GLU* 3.8 7.3 + - - +
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Residues in contact with GLU 525 (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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523B SER* 3.7 3.5 + - - +
524B ASP* 1.3 76.1 - - - +
526B ILE* 1.3 62.7 + - + +
528B GLU* 5.0 2.0 - - - -
529B LYS* 4.1 17.4 + - + +
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Residues in contact with ILE 526 (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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514B LEU* 4.6 2.5 - - + -
516B VAL* 4.3 23.1 - - + -
520B PHE 5.7 0.7 - - - +
521B ASP 5.3 0.2 - - - +
522B PHE* 3.4 25.8 - - + -
523B SER* 3.1 36.1 - - - +
524B ASP 2.5 6.9 + - - -
525B GLU* 1.3 82.0 - - + +
527B LYS* 1.3 61.2 + - - +
528B GLU 3.3 2.2 - - - -
529B LYS* 3.2 13.4 + - + +
530B ILE* 2.8 31.9 + - + +
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Residues in contact with LYS 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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498B ILE* 4.5 20.8 - - + +
522B PHE 3.4 23.1 - - - +
523B SER* 2.7 35.0 + - - +
524B ASP* 3.1 26.2 + - - +
526B ILE* 1.3 73.9 - - - +
528B GLU* 1.3 60.7 + - - +
530B ILE* 3.6 11.7 + - - +
531B LYS* 3.4 28.0 + - - +
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Residues in contact with GLU 528 (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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524B ASP 3.8 7.3 + - - +
525B GLU 5.9 1.1 - - - -
526B ILE 3.3 0.8 - - - -
527B LYS* 1.3 75.6 - - - +
529B LYS* 1.3 61.3 + - - +
530B ILE 3.0 6.0 + - - -
531B LYS* 3.3 38.8 + - + +
532B LYS* 3.4 11.2 - - + +
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Residues in contact with LYS 529 (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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514B LEU* 3.5 22.4 - - + +
525B GLU* 4.1 16.0 + - + +
526B ILE* 3.2 10.3 + - + +
528B GLU* 1.3 77.4 - - - +
530B ILE* 1.3 59.0 + - - +
532B LYS* 3.1 31.2 + - + +
533B LEU* 5.1 1.9 - - - +
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Residues in contact with ILE 530 (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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498B ILE* 4.1 18.6 - - + -
499B ILE* 3.8 40.2 - - + -
502B ALA* 4.2 9.7 - - + +
514B LEU* 3.3 29.4 - - + -
522B PHE* 3.8 16.2 - - + -
526B ILE* 2.8 42.8 - - + +
527B LYS* 3.6 7.4 - - - +
528B GLU 3.0 0.2 - - - -
529B LYS* 1.3 75.7 - - - +
531B LYS* 1.3 54.3 + - - +
532B LYS 2.7 15.6 + - - -
533B LEU* 3.4 18.1 + - + +
538B LEU* 4.8 3.9 - - + +
541B MET* 5.8 0.4 - - + -
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Residues in contact with LYS 531 (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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502B ALA* 3.9 22.4 - - + +
505B ASN* 5.2 6.2 - - - +
506B PRO* 6.0 0.4 - - - +
507B ASN* 4.8 9.2 + - - +
527B LYS* 3.4 18.1 + - - +
528B GLU* 3.3 33.0 + - + +
530B ILE* 1.3 76.9 - - - +
532B LYS* 1.3 57.3 + - + +
533B LEU 3.8 1.7 + - - -
107J G 6.0 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