Contacts of the helix formed by residues 493 - 497 (chain A) in PDB entry 3L4U
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 GLN 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A VAL* 4.9 4.2 - - - +
481A THR* 4.0 7.9 + - - -
482A LEU* 4.1 22.0 - - + +
483A CYS 3.2 27.4 - - - +
484A MET* 3.5 16.5 + - + +
486A ALA* 2.9 17.9 + - + +
488A GLN* 3.2 27.1 + - - +
491A GLY 3.9 0.6 + - - -
492A LYS* 1.3 72.8 - - - +
494A TYR* 1.3 62.4 + - - +
496A ILE* 4.1 4.7 - - - -
497A HIS* 2.8 72.2 + - - +
500A TYR* 5.2 3.6 - - - +
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Residues in contact with TYR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLN* 3.0 31.1 + - + +
200A PHE* 5.3 3.1 - - - -
238A SER 4.8 0.5 - - - +
239A ASN* 3.3 31.0 - - - +
240A ALA 4.9 2.8 + - - -
256A ILE* 2.5 60.7 + - + +
257A GLY* 4.4 2.7 - - - -
463A LEU* 3.5 37.9 - - + -
466A PRO* 4.1 3.6 - - + +
477A LEU* 3.9 9.4 - - + -
484A MET* 2.9 30.5 + - + +
492A LYS* 3.8 23.6 - - - -
493A GLN* 1.3 76.3 - - - +
495A ASP* 1.3 67.4 + - - +
497A HIS* 4.8 2.6 + - - +
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Residues in contact with ASP 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 3.6 45.6 - - + +
238A SER* 2.6 37.3 + - - +
239A ASN* 2.9 23.9 + - - +
257A GLY* 5.0 0.2 - - - -
258A GLY 4.5 3.5 + - - -
491A GLY* 5.8 0.3 - - - -
492A LYS* 2.9 43.4 + - + +
494A TYR* 1.3 84.9 - - - +
496A ILE* 1.3 58.6 + - + +
497A HIS 3.6 0.9 - - - -
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Residues in contact with ILE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 3.6 33.0 - - + -
416A THR* 4.3 6.3 - - + -
488A GLN* 3.2 52.6 + - + +
490A TRP* 4.0 26.0 - - + +
491A GLY* 3.4 11.9 - - - +
492A LYS 3.1 16.5 + - - +
493A GLN* 4.1 1.1 - - - -
495A ASP* 1.3 77.3 - - + +
497A HIS* 1.3 68.4 + - - +
498A ASN 3.3 2.2 - - - -
499A LEU* 2.9 31.9 + - + +
500A TYR* 3.7 4.2 + - - +
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Residues in contact with HIS 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PHE* 3.4 35.5 - + + -
201A ASN* 2.7 36.7 + - + -
238A SER 5.5 0.9 - - - +
446A GLU 3.3 27.5 + - - +
481A THR* 3.2 30.5 + - + +
484A MET* 4.1 1.3 - - + -
493A GLN* 2.8 52.0 + - + +
494A TYR 5.0 2.0 - - - +
495A ASP 3.6 1.6 - - - -
496A ILE* 1.3 77.4 - - - +
498A ASN* 1.3 71.3 + - - +
499A LEU 3.1 5.0 + - - -
500A TYR* 3.2 13.7 + - - +
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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