Contacts of the helix formed by residues 495 - 503 (chain A) in PDB entry 4L28
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 THR 495 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A TRP* 3.8 15.3 + - - -
411A HIS* 5.1 13.0 - - - +
412A LEU 3.2 8.3 - - - +
413A ARG* 4.6 15.7 - - - +
414A VAL* 4.1 4.8 - - - +
493A THR 4.9 1.1 - - - +
494A ASP* 1.3 76.6 + - - +
496A LEU* 1.3 63.6 + - - +
497A GLY* 3.6 1.9 + - - -
498A ARG* 3.1 30.3 + - - +
499A LEU 3.3 7.4 + - - -
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TRP* 3.4 50.4 - - + +
410A TRP 3.8 0.8 + - - -
412A LEU* 2.7 30.7 + - + +
413A ARG 4.3 2.5 - - - +
414A VAL* 4.4 11.0 - - + -
416A GLU* 6.2 0.2 - - + -
417A LEU* 3.7 30.1 - - + -
495A THR* 1.3 73.1 - - - +
497A GLY* 1.3 58.8 + - - +
499A LEU* 3.1 18.9 + - + +
500A SER* 2.9 21.7 + - - -
539A LEU* 4.0 13.0 - - + +
542A PHE* 3.8 26.0 - - + -
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Residues in contact with GLY 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TRP* 4.1 0.4 - - - -
410A TRP* 3.4 53.7 + - - -
495A THR* 3.1 2.7 + - - -
496A LEU* 1.3 76.5 - - - +
498A ARG* 1.3 63.5 + - - +
500A SER* 3.0 4.4 + - - -
501A HIS* 2.9 27.5 + - - -
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Residues in contact with ARG 498 (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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488A LYS* 5.3 9.3 - - - +
490A ILE* 4.9 1.1 - - + +
494A ASP* 4.5 20.7 + - + +
495A THR* 3.1 26.7 + - - +
497A GLY* 1.3 75.6 - - - +
499A LEU* 1.3 58.9 + - - +
501A HIS* 3.1 22.9 + - - +
502A ILE* 2.9 65.6 + - + +
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Residues in contact with LEU 499 (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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414A VAL* 4.8 7.2 - - + -
417A LEU* 4.4 5.8 - - + -
490A ILE* 3.8 15.7 - - + -
494A ASP* 6.0 0.2 - - - +
495A THR 3.3 6.0 + - - +
496A LEU* 3.1 32.8 + - + +
498A ARG* 1.3 79.2 - - - +
500A SER* 1.3 57.7 + - - +
502A ILE* 3.0 9.8 + - + +
503A LEU* 2.9 46.2 + - + +
509A ALA* 3.6 31.4 - - + -
534A VAL* 4.0 24.7 - - + -
539A LEU* 4.2 21.1 - - + -
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Residues in contact with SER 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TRP* 3.8 16.5 - - - -
410A TRP* 3.9 20.9 - - - -
496A LEU 2.9 12.1 + - - -
497A GLY 3.0 9.4 + - - -
499A LEU* 1.3 79.4 - - - +
501A HIS* 1.3 60.6 + - - +
503A LEU* 3.6 10.2 + - - +
504A GLU* 3.5 21.5 + - - +
539A LEU* 4.4 11.5 - - - +
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Residues in contact with HIS 501 (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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388A ASP* 5.2 10.3 - - + -
406A LYS* 4.6 9.3 + - - -
410A TRP* 3.9 22.7 - + - -
497A GLY 2.9 23.4 + - - -
498A ARG* 3.1 22.4 + - - +
500A SER* 1.3 78.3 - - - +
502A ILE* 1.3 62.3 + - - +
504A GLU* 3.3 33.2 + - - +
505A MET* 4.1 6.2 + - - +
182C ARG* 4.0 16.9 + - - +
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Residues in contact with ILE 502 (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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488A LYS* 3.6 38.4 - - + -
489A GLN 4.2 1.3 - - - +
490A ILE* 3.4 32.5 - - + -
498A ARG* 2.9 43.8 + - + +
499A LEU* 3.0 10.0 + - + +
501A HIS* 1.3 73.1 - - - +
503A LEU* 1.3 58.8 + - + +
504A GLU 3.0 4.5 - - - -
505A MET* 3.0 8.9 + - - +
506A ASP* 3.0 28.4 + - + +
509A ALA* 4.5 15.7 - - + -
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Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A LEU* 2.9 39.3 + - + +
500A SER* 4.1 7.0 - - - +
501A HIS 3.2 0.8 - - - -
502A ILE* 1.3 78.0 - - + +
504A GLU* 1.3 60.5 + - - +
505A MET 3.2 0.4 - - - -
506A ASP 3.2 22.9 - - - +
507A HIS* 3.6 18.1 - - - +
508A PHE 4.8 0.4 - - - -
509A ALA* 4.4 13.0 - - + -
534A VAL 4.2 9.2 - - - +
535A THR 3.9 4.7 - - - +
536A ALA* 3.6 41.3 - - + +
539A LEU* 4.4 10.1 - - + -
188C ILE 3.9 7.0 - - - +
189C VAL* 4.0 0.9 - - - +
190C ARG* 3.5 19.1 + - - +
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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