Contacts of the helix formed by residues 498 - 529 (chain H) in PDB entry 5KHU
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 498 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497H ASN* 3.8 29.4 - - - +
499H GLY* 3.7 29.4 - - - +
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Residues in contact with GLY 499 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498H THR* 3.7 29.2 - - - +
500H TRP* 3.8 25.4 - - - +
502H LEU* 4.3 19.7 - - - +
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Residues in contact with TRP 500 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499H GLY* 3.8 25.8 - - - +
501H VAL* 3.8 29.2 - - - +
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Residues in contact with VAL 501 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500H TRP* 3.8 29.8 - - - +
502H LEU* 3.8 26.0 - - - +
504H GLN* 4.3 18.8 - - - +
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Residues in contact with LEU 502 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499H GLY* 4.3 15.5 - - - +
501H VAL* 3.8 24.5 - - - +
503H CYS* 3.7 29.8 - - - +
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Residues in contact with CYS 503 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502H LEU* 3.7 29.2 - - - +
504H GLN* 3.8 26.5 - - - +
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Residues in contact with GLN 504 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501H VAL* 4.3 16.6 - - - +
503H CYS* 3.8 24.7 - - - +
505H ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 505 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504H GLN* 3.8 25.6 - - - +
506H GLY* 3.8 30.3 - - - +
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Residues in contact with GLY 506 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505H ILE* 3.8 29.4 - - - +
507H ARG* 3.8 25.8 - - - +
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Residues in contact with ARG 507 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506H GLY* 3.8 29.8 - - - +
508H ALA* 3.8 25.1 - - - +
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Residues in contact with ALA 508 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507H ARG* 3.8 28.7 - - - +
509H TYR* 3.8 27.1 - - - +
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Residues in contact with TYR 509 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508H ALA* 3.8 25.4 - - - +
510H PHE* 3.8 29.6 - - - +
512H LEU* 4.3 15.7 - - - +
514H GLU* 4.7 15.3 - - - +
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Residues in contact with PHE 510 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509H TYR* 3.8 29.6 - - - +
511H GLU* 3.8 26.0 - - - +
513H SER* 4.1 18.6 - - - +
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Residues in contact with GLU 511 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510H PHE* 3.8 23.1 - - - +
512H LEU* 3.7 30.1 - - - +
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Residues in contact with LEU 512 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509H TYR* 4.3 17.3 - - - +
511H GLU* 3.7 29.6 - - - +
513H SER* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with SER 513 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510H PHE* 4.1 18.8 - - - +
512H LEU* 3.8 26.2 - - - +
514H GLU* 3.8 28.7 - - - +
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Residues in contact with GLU 514 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509H TYR* 4.7 16.4 - - - +
513H SER* 3.8 26.7 - - - +
515H TYR* 3.7 29.6 - - - +
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Residues in contact with TYR 515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514H GLU* 3.7 29.8 - - - +
516H MET* 3.7 29.8 - - - +
517H GLN* 4.7 0.7 - - - +
518H ALA* 4.3 18.6 - - - +
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Residues in contact with MET 516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515H TYR* 3.7 29.4 - - - +
517H GLN* 3.7 22.9 - - - +
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Residues in contact with GLN 517 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515H TYR* 4.7 4.9 - - - +
516H MET* 3.7 29.8 - - - +
518H ALA* 3.8 26.7 - - - +
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Residues in contact with ALA 518 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515H TYR* 4.3 15.5 - - - +
517H GLN* 3.8 28.0 - - - +
519H GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 519 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518H ALA* 3.8 26.5 - - - +
520H ARG* 3.8 29.8 - - - +
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Residues in contact with ARG 520 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519H GLU* 3.8 29.2 - - - +
521H ILE* 3.8 28.0 - - - +
----------------------------------------------------------
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Residues in contact with ILE 521 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520H ARG* 3.8 24.9 - - - +
522H PHE* 3.8 29.2 - - - +
524H GLU* 4.7 14.8 - - - +
----------------------------------------------------------
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Residues in contact with PHE 522 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521H ILE* 3.8 28.7 - - - +
523H SER* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with SER 523 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522H PHE* 3.8 29.2 - - - +
524H GLU* 3.8 25.4 - - - +
526H ARG* 4.4 15.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 524 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521H ILE* 4.7 15.3 - - - +
523H SER* 3.8 29.2 - - - +
525H VAL* 3.8 26.7 - - - +
----------------------------------------------------------
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Residues in contact with VAL 525 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524H GLU* 3.8 25.6 - - - +
526H ARG* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with ARG 526 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523H SER* 4.4 19.7 - - - +
525H VAL* 3.8 25.4 - - - +
527H ARG* 3.7 29.8 - - - +
----------------------------------------------------------
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Residues in contact with ARG 527 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526H ARG* 3.7 29.6 - - - +
528H ILE* 3.8 28.7 - - - +
----------------------------------------------------------
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Residues in contact with ILE 528 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527H ARG* 3.8 29.2 - - - +
529H GLU* 3.8 27.1 - - - +
----------------------------------------------------------
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Residues in contact with GLU 529 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528H ILE* 3.8 28.7 - - - +
530H ASN* 3.8 28.9 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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