Contacts of the helix formed by residues 510 - 522 (chain D) in PDB entry 3UK3
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 510 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B T 3.4 54.3 + - + +
16B C 3.2 28.2 + - - +
485D TYR* 3.2 23.8 + - - -
488D ILE* 3.4 33.1 + - + +
489D HIS* 4.9 2.2 - - - +
491D ARG* 5.0 0.7 - - - +
492D THR* 6.1 0.8 - - - -
499D TYR* 3.8 6.8 - - - -
508D ALA* 3.6 15.5 - - - +
509D ALA* 1.3 83.2 - - + +
511D LYS* 1.3 66.3 + - - +
512D THR 3.2 2.2 + - - +
513D SER* 3.4 9.8 + - - -
514D LEU* 3.7 1.0 + - - +
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Residues in contact with LYS 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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5A C 3.6 37.0 + - - +
6A A 6.3 0.2 - - - +
499D TYR* 3.4 44.8 - - + +
510D GLN* 1.3 74.1 - - - +
512D THR* 1.3 62.9 + - - +
514D LEU* 3.3 6.9 + - + +
515D ARG* 3.1 34.8 + - - +
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Residues in contact with THR 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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6A A 3.8 3.6 + - - -
7A G 2.6 39.2 + - + +
8A A 3.8 7.2 - - - +
14B T 4.6 7.0 - - + -
15B T 3.2 28.5 - - + +
16B C 4.3 2.1 + - - -
510D GLN* 3.2 1.6 - - - +
511D LYS* 1.3 79.2 - - - +
513D SER* 1.3 56.6 + - - +
515D ARG* 3.3 27.1 + - - +
516D TYR* 3.0 29.6 + - + +
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Residues in contact with SER 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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14B T 3.5 41.3 + - - +
15B T 3.3 23.2 + - - +
506D TYR* 3.4 19.0 + - - -
508D ALA* 3.7 6.5 - - - -
509D ALA 5.4 0.2 - - - -
510D GLN* 3.4 11.3 + - - +
511D LYS 3.3 0.6 - - - -
512D THR* 1.3 79.3 - - - +
514D LEU* 1.3 56.9 + - - +
516D TYR* 3.5 3.3 + - - +
517D HIS* 2.9 27.9 + - - +
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Residues in contact with LEU 514 (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 TYR* 3.8 28.9 - - + +
500D LYS 3.8 16.2 - - - +
501D CYS* 3.8 32.1 - - + +
506D TYR* 3.9 17.9 - - + -
508D ALA* 3.9 11.6 - - + +
510D GLN 3.7 1.8 + - - +
511D LYS* 3.3 9.0 + - + +
513D SER* 1.3 75.6 - - - +
515D ARG* 1.3 60.2 + - - +
517D HIS* 3.1 5.0 + - + +
518D LEU* 2.8 45.5 + - + +
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Residues in contact with ARG 515 (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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5A C 4.7 2.6 - - - +
6A A 3.4 57.8 + - - +
7A G 5.0 3.9 + - - -
511D LYS* 3.1 20.8 + - - +
512D THR* 3.3 40.1 + - + +
514D LEU* 1.3 78.1 - - - +
516D TYR* 1.3 62.0 + - - +
518D LEU* 3.4 13.9 + - - +
519D GLU* 3.1 33.6 + - - +
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Residues in contact with TYR 516 (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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12B G 3.0 19.1 + - + +
13B A 2.6 59.8 + + + -
14B T 3.6 26.5 - - + -
512D THR* 3.0 18.3 + - + +
513D SER 3.8 2.9 - - - +
515D ARG* 1.3 77.1 - - - +
517D HIS* 1.3 69.1 + - + +
519D GLU* 3.3 7.2 + - + +
520D ARG* 3.2 46.8 + - + +
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Residues in contact with HIS 517 (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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14B T 5.4 0.9 - - - +
501D CYS* 3.8 6.3 - - + -
504D CYS* 3.3 8.6 - - - -
506D TYR* 3.4 47.9 - + + +
513D SER 2.9 19.0 + - - +
514D LEU* 3.3 6.7 - - + +
516D TYR* 1.3 82.7 - - + +
518D LEU* 1.3 58.5 + - - +
520D ARG* 5.3 0.9 - - - -
521D HIS* 3.0 56.6 + + + +
522D HIS* 3.7 1.0 + + - -
967D ZN 2.4 35.7 - - - -
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Residues in contact with LEU 518 (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 CYS* 4.3 12.1 - - - -
502D GLU* 5.6 2.7 - - + +
503D PHE* 3.9 32.8 - - + -
514D LEU* 2.8 33.3 + - + +
515D ARG* 3.6 13.2 - - - +
517D HIS* 1.3 76.3 - - - +
519D GLU* 1.3 61.0 - - - +
522D HIS* 3.0 44.4 + - + +
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Residues in contact with GLU 519 (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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515D ARG* 3.1 27.5 + - + +
516D TYR* 3.3 8.2 + - + +
518D LEU* 1.3 77.9 - - - +
520D ARG* 1.3 78.0 + - + +
522D HIS 5.0 0.4 - - - -
523D LYS* 3.6 20.5 - - - +
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Residues in contact with ARG 520 (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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13B A 5.3 2.7 - - - +
516D TYR* 3.2 44.9 + - + +
517D HIS* 4.6 0.9 - - - +
519D GLU* 1.3 102.0 + - + +
521D HIS* 1.3 59.8 + - - +
522D HIS 3.6 0.9 - - - -
523D LYS* 5.2 8.2 + - - +
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Residues in contact with HIS 521 (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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1D ZN 3.2 36.9 - - - -
504D CYS* 5.5 6.3 - - + -
517D HIS* 3.0 38.0 + + + +
520D ARG* 1.3 75.6 - - - +
522D HIS* 1.3 77.1 + + + +
523D LYS 3.8 2.6 + - - -
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Residues in contact with HIS 522 (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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1D ZN 4.4 6.2 - - - -
501D CYS* 3.9 7.0 - - - -
503D PHE* 3.5 40.7 - + + +
504D CYS* 4.3 8.1 - - + -
517D HIS* 3.7 7.7 + + - -
518D LEU* 3.0 30.2 + - + +
521D HIS* 1.3 99.6 + + - +
523D LYS* 1.3 61.2 + - - +
967D ZN 2.0 37.3 - - - -
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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