Contacts of the helix formed by residues 521 - 526 (chain B) in PDB entry 3L5J
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 PRO 521 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B ASP* 3.4 20.9 - - + +
519B GLN 3.2 8.5 - - - +
520B LEU* 1.3 87.9 - - + +
522B VAL* 1.3 55.5 + - - +
523B ASP* 2.7 28.7 + - + +
524B VAL* 3.0 27.2 + - + +
525B GLN 3.5 3.3 + - - -
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Residues in contact with VAL 522 (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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438B LEU* 4.4 21.1 - - + +
439B SER* 6.0 0.2 - - - -
440B ASP* 3.9 15.4 + - - +
467B SER 5.6 0.7 - - - +
469B CYS* 4.3 18.4 + - + +
491B TYR* 4.1 18.1 + - - +
520B LEU 3.4 2.0 + - - +
521B PRO* 1.3 70.2 - - - +
523B ASP* 1.3 66.7 + - - +
524B VAL 3.4 0.6 + - - -
525B GLN* 3.5 31.4 + - - +
526B ASN 4.2 3.1 + - - -
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Residues in contact with ASP 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU 5.6 1.6 - - - -
439B SER* 3.0 18.6 + - - +
440B ASP* 3.0 42.8 + - - +
441B LYS* 4.2 9.4 + - - +
467B SER 4.8 3.1 - - - +
521B PRO* 2.7 15.0 + - + +
522B VAL* 1.3 76.3 - - - +
524B VAL* 1.3 65.6 + - + +
526B ASN* 3.2 15.2 + - - +
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B PRO* 3.3 4.0 - - - +
498B SER* 3.0 44.0 + - - +
499B LYS* 3.9 25.4 - - + +
520B LEU* 4.1 11.0 - - + -
521B PRO* 3.0 30.7 + - + +
523B ASP* 1.3 83.4 - - + +
525B GLN* 1.3 62.3 + - - +
526B ASN* 3.4 3.7 - - - +
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Residues in contact with GLN 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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491B TYR* 4.4 6.1 + - - +
495B ALA 3.6 4.3 - - - +
497B PRO* 3.4 19.1 - - - +
519B GLN* 5.7 4.0 + - - +
520B LEU* 2.8 37.4 + - + +
521B PRO 3.5 4.0 + - - +
522B VAL* 3.8 28.0 - - - +
523B ASP 3.4 1.0 - - - -
524B VAL* 1.3 75.8 - - - +
526B ASN* 1.3 65.8 + - - +
527B GLY 3.0 23.6 + - - +
528B PHE* 4.7 1.2 - - - -
529B ILE* 3.5 33.2 + - + +
574B THR* 3.7 7.4 - - - +
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Residues in contact with ASN 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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467B SER* 3.4 39.2 + - - +
491B TYR* 3.5 9.8 + - - -
494B GLN* 3.2 7.3 - - - -
495B ALA* 2.8 38.1 + - + +
496B PRO 3.6 14.4 + - - +
498B SER* 3.9 18.5 + - - +
522B VAL 4.2 3.2 + - - -
523B ASP 3.2 20.2 + - - +
524B VAL* 3.6 7.2 - - - -
525B GLN* 1.3 80.3 - - - +
527B GLY* 1.3 54.7 + - - +
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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