Contacts of the helix formed by residues 499 - 513 (chain D) in PDB entry 4K9N
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 ASN 499 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350D ALA* 3.5 26.3 + - - +
351D GLY 3.8 4.5 - - - +
353D LEU* 3.5 13.5 - - - +
497D ALA 3.4 1.2 - - - -
498D ASP* 1.3 84.3 + - - +
500D LEU* 1.3 60.5 + - - +
501D GLU* 3.1 13.8 + - - +
502D GLN* 2.9 39.7 + - - +
503D LEU* 2.8 27.4 + - - +
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Residues in contact with LEU 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D GLN* 4.3 20.8 - - + +
349D ASP 5.5 2.6 + - - +
351D GLY 4.8 1.0 + - - -
353D LEU* 3.8 17.5 - - + +
357D THR* 3.6 29.8 - - + -
361D THR* 3.7 12.6 - - - +
499D ASN* 1.3 76.0 - - - +
501D GLU* 1.3 62.9 + - - +
503D LEU* 3.1 3.2 + - + +
504D LYS* 2.9 60.2 + - + +
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Residues in contact with GLU 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D ASN* 3.1 10.7 + - - +
500D LEU* 1.3 78.6 - - - +
502D GLN* 1.3 65.8 + - + +
504D LYS* 3.5 8.3 + - - +
505D GLY* 3.1 18.9 + - - -
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Residues in contact with GLN 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D LYS* 4.3 7.0 - - - +
497D ALA* 3.7 14.0 + - - -
498D ASP* 2.7 43.1 + - - +
499D ASN* 2.9 29.7 + - - +
501D GLU* 1.3 76.9 - - + +
503D LEU* 1.3 60.4 + - - +
505D GLY* 3.2 1.1 + - - +
506D SER* 2.8 35.9 + - - +
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Residues in contact with LEU 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D LEU* 3.6 25.6 - - + -
358D VAL* 4.0 20.6 - - + -
361D THR* 3.8 31.6 - - + +
451D VAL* 5.6 2.2 - - + -
497D ALA* 3.7 10.9 - - + +
499D ASN 2.8 13.5 + - - +
500D LEU* 3.1 9.6 + - + +
502D GLN* 1.3 76.1 - - - +
504D LYS* 1.3 63.2 + - - +
506D SER* 3.8 1.0 - - - -
507D LEU* 2.9 46.1 + - + +
519D ILE* 5.1 4.3 - - + -
521D VAL* 4.0 28.5 - - + -
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Residues in contact with LYS 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D THR* 4.1 8.3 - - + -
365D MET* 3.7 33.6 - - + +
500D LEU* 2.9 50.4 + - + +
501D GLU* 3.8 7.4 - - - +
503D LEU* 1.3 78.0 - - - +
505D GLY* 1.3 63.0 + - - +
507D LEU* 3.9 1.8 - - - +
508D GLN* 3.0 25.1 + - - +
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Residues in contact with GLY 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D GLU 3.1 15.7 + - - -
502D GLN* 3.2 2.7 + - - -
504D LYS* 1.3 74.8 - - - +
506D SER* 1.3 56.5 + - - +
508D GLN* 3.2 13.5 + - - +
509D GLU* 2.9 29.1 + - - +
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Residues in contact with SER 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D LEU* 3.6 22.9 - - - +
496D LYS 2.8 26.0 + - - -
502D GLN* 2.8 19.0 + - - +
503D LEU* 3.8 4.3 - - - -
505D GLY* 1.3 69.7 - - - +
507D LEU* 1.3 59.9 + - - +
509D GLU* 3.2 3.3 + - - +
510D ALA* 2.8 30.1 + - - +
519D ILE* 4.0 24.0 - - - -
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Residues in contact with LEU 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D THR* 4.0 20.6 - - + -
362D LEU* 3.7 35.7 - - + +
365D MET* 4.0 13.2 - - + -
423D ILE* 5.8 2.7 - - + -
449D ILE* 5.3 4.5 - - + -
451D VAL* 4.8 7.4 - - + -
503D LEU* 2.9 47.5 + - + +
504D LYS 3.9 3.4 - - - +
506D SER* 1.3 76.2 - - - +
508D GLN* 1.3 63.0 + - - +
510D ALA* 3.3 2.9 + - + +
511D LEU* 3.0 40.6 + - + +
519D ILE* 4.0 17.9 - - + -
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Residues in contact with GLN 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D MET* 4.7 6.9 - - + +
504D LYS 3.0 18.2 + - - +
505D GLY* 3.3 10.9 + - - +
507D LEU* 1.3 79.1 - - - +
509D GLU* 1.3 63.6 + - - +
511D LEU* 3.7 6.8 + - - +
512D SER* 3.4 22.8 + - - +
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Residues in contact with GLU 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D GLN* 3.3 27.3 + - - +
495D LEU* 3.8 21.6 - - + +
505D GLY 2.9 14.3 + - - +
506D SER* 3.7 6.9 - - - +
508D GLN* 1.3 77.5 - - - +
510D ALA* 1.3 63.7 + - - +
512D SER* 3.1 6.6 + - - -
513D ALA* 3.0 22.1 + - + +
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Residues in contact with ALA 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D GLN* 5.4 0.5 - - - +
449D ILE* 3.8 24.9 - - + +
495D LEU* 4.4 0.8 - - - +
506D SER 2.8 17.0 + - - +
507D LEU* 3.7 4.5 - - + +
509D GLU* 1.3 76.7 - - - +
511D LEU* 1.3 63.4 + - - +
513D ALA* 3.2 18.4 + - - +
515D GLY 5.2 0.7 - - - +
517D VAL* 3.9 29.3 - - + +
519D ILE* 3.8 20.2 - - + -
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Residues in contact with LEU 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D MET* 3.8 39.0 - - + +
366D ALA* 4.4 1.3 - - + +
367D PRO* 4.0 17.0 - - + -
421D GLN* 3.9 25.0 - - + +
423D ILE* 4.7 8.5 - - + -
449D ILE* 3.9 19.7 - - + -
507D LEU* 3.0 29.5 + - + +
508D GLN* 4.2 5.8 - - - +
509D GLU 3.3 0.2 - - - -
510D ALA* 1.3 75.9 - - - +
512D SER* 1.3 61.0 + - - +
513D ALA 3.8 5.4 - - - +
514D LYS* 5.2 2.8 + - - -
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Residues in contact with SER 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508D GLN* 3.4 14.2 + - - +
509D GLU* 3.1 11.3 + - - -
511D LEU* 1.3 76.5 - - - +
513D ALA* 1.3 67.7 + - - +
514D LYS* 3.7 19.6 + - - +
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Residues in contact with ALA 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D GLN* 5.6 1.4 - - - +
447D PRO* 5.5 2.3 - - - +
493D GLN* 4.2 14.1 - - - +
509D GLU* 3.0 11.5 + - + +
510D ALA* 3.2 16.5 + - - +
511D LEU 3.8 6.8 - - - +
512D SER* 1.3 82.3 - - - +
514D LYS* 1.3 65.4 + - - +
515D GLY 3.5 6.0 + - - +
517D VAL* 3.6 24.7 - - + -
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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