Contacts of the helix formed by residues 510 - 522 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A T 3.5 52.4 + - + +
16A C 3.2 29.9 + - - +
485C TYR* 3.1 26.6 + - - -
488C ILE* 3.6 31.0 + - + +
489C HIS* 5.1 1.4 - - - +
491C ARG* 4.9 0.2 - - - +
492C THR* 6.1 1.2 - - - -
499C TYR* 3.6 6.2 - - - -
508C ALA* 3.7 5.3 - - - +
509C ALA* 1.3 82.6 - - + +
511C LYS* 1.3 66.7 + - - +
512C THR 3.3 1.6 - - - +
513C SER* 3.2 18.5 + - - +
514C LEU 3.6 3.8 + - - -
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Residues in contact with LYS 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B C 3.1 54.7 + - + +
6B A 4.8 7.0 + - - +
499C TYR* 3.4 44.2 - - + +
510C GLN* 1.3 73.4 - - - +
512C THR* 1.3 58.3 + - - +
514C LEU* 3.2 5.9 + - + +
515C ARG* 2.9 47.9 + - + +
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Residues in contact with THR 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A T 4.5 9.6 - - + +
15A T 3.2 26.7 - - - +
16A C 4.3 1.7 + - - -
6B A 3.9 3.8 + - - -
7B G 2.5 39.9 + - - +
8B A 4.0 4.9 - - - +
510C GLN* 3.3 1.6 - - - +
511C LYS* 1.3 78.3 - - - +
513C SER* 1.3 58.0 + - - +
515C ARG* 3.3 27.7 + - + +
516C TYR* 2.9 29.0 + - + +
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Residues in contact with SER 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A A 5.8 0.5 - - - +
14A T 3.6 38.2 + - - +
15A T 3.2 24.3 + - - +
506C TYR* 3.3 23.5 + - - -
508C ALA* 3.7 7.6 - - - -
509C ALA 5.4 0.2 - - - -
510C GLN 3.2 11.3 + - - -
512C THR* 1.3 78.2 - - - +
514C LEU* 1.3 57.3 + - - +
516C TYR* 3.4 2.6 + - - +
517C HIS* 2.9 24.4 + - - +
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Residues in contact with LEU 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499C TYR* 3.7 39.0 - - + -
500C LYS 4.0 16.2 - - - +
501C CYS* 3.8 24.5 - - - +
506C TYR* 3.9 21.0 + - + -
508C ALA* 3.9 1.9 - - + +
510C GLN 3.6 2.0 + - - -
511C LYS* 3.2 10.1 + - + +
513C SER* 1.3 75.1 - - - +
515C ARG* 1.3 60.6 + - - +
517C HIS* 3.2 1.2 + - - +
518C LEU* 2.9 60.7 + - + +
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Residues in contact with ARG 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B A 3.5 43.2 + - - +
7B G 3.6 27.8 + - - -
511C LYS* 2.9 30.4 + - + +
512C THR* 3.3 36.1 + - - +
514C LEU* 1.3 78.9 - - - +
516C TYR* 1.3 62.8 + - - +
518C LEU* 3.5 6.0 + - - +
519C GLU* 3.2 28.5 + - - +
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Residues in contact with TYR 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A G 3.5 32.0 + + + +
13A A 3.7 32.5 - + + -
14A T 3.6 22.7 - - + -
512C THR* 2.9 18.2 + - + +
513C SER 3.7 2.9 - - - +
515C ARG* 1.3 74.6 - - - +
517C HIS* 1.3 69.9 + - - +
519C GLU* 3.2 23.1 + - + +
520C ARG* 3.4 55.4 + - + +
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Residues in contact with HIS 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C CYS* 3.9 5.8 - - - -
504C CYS* 3.3 4.9 - - - -
506C TYR* 3.4 52.6 - + + +
513C SER 2.9 17.4 + - - +
514C LEU 3.4 4.3 - - - +
516C TYR* 1.3 80.6 - - - +
518C LEU* 1.3 68.6 + - + +
521C HIS* 3.1 63.0 + + + +
522C HIS* 3.1 9.2 + + - -
967C ZN 2.1 37.5 - - - -
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Residues in contact with LEU 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C CYS* 4.6 6.1 - - + -
502C GLU* 5.7 2.9 - - + +
503C PHE* 3.9 33.9 - - + -
514C LEU* 2.9 57.6 + - + +
515C ARG* 3.9 6.5 - - - +
517C HIS* 1.3 83.9 - - + +
519C GLU* 1.3 62.9 + - - +
522C HIS* 3.1 42.4 + - + +
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Residues in contact with GLU 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C ARG* 3.2 17.1 + - - +
516C TYR* 3.2 20.7 + - + +
518C LEU* 1.3 82.5 - - - +
520C ARG* 1.3 63.8 + - + +
522C HIS 4.3 6.6 - - - -
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Residues in contact with ARG 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A G 4.1 32.7 + - - -
13A A 3.3 25.4 + - - -
516C TYR* 3.4 38.7 + - + +
519C GLU* 1.3 80.9 - - + +
521C HIS* 1.3 86.2 + - + +
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Residues in contact with HIS 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A A 3.4 22.6 + - - -
1C ZN 2.1 37.8 - - - -
517C HIS* 3.1 49.8 + + + +
520C ARG* 1.3 91.8 + - + +
522C HIS* 1.3 80.1 + - + +
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Residues in contact with HIS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C CYS* 3.9 6.3 - - - -
503C PHE* 3.4 38.4 - + + +
504C CYS* 4.2 6.1 - - + -
517C HIS* 3.1 19.2 + + - -
518C LEU* 3.1 36.1 + - + +
519C GLU 4.3 7.4 - - - -
521C HIS* 1.3 91.2 + - + +
967C ZN 2.2 35.7 - - - -
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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