Contacts of the helix formed by residues 510 - 523 (chain C) in PDB entry 3HZJ
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 LEU 510 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511C TYR* 1.3 67.3 + - - +
512C SER* 3.4 7.2 - - - +
513C TRP* 3.4 36.2 + - + +
514C GLY* 3.2 17.3 + - - -
534C LEU* 4.5 12.1 - - + -
543C LEU* 6.1 2.0 - - - +
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Residues in contact with TYR 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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510C LEU* 1.3 74.1 - - - +
512C SER* 1.3 59.8 + - - +
514C GLY* 2.9 19.9 + - - -
515C GLU* 3.2 26.1 + - - +
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Residues in contact with SER 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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510C LEU* 3.4 7.9 - - - +
511C TYR* 1.3 78.0 - - - +
513C TRP* 1.3 61.4 + - - +
515C GLU* 3.4 10.1 + - - +
516C LEU* 3.1 28.8 + - - +
534C LEU* 3.8 30.2 - - - +
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Residues in contact with TRP 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C LEU* 3.4 33.2 + - + +
511C TYR 3.2 0.6 - - - -
512C SER* 1.3 73.6 - - - +
514C GLY* 1.3 65.7 + - - +
516C LEU* 3.3 11.4 + - + +
517C LEU* 3.1 31.6 + - + +
520C TRP* 4.2 27.1 - + - -
534C LEU* 3.4 46.2 + - + +
535C VAL* 4.0 15.7 - - + -
538C GLY 4.1 1.0 + - - -
539C VAL* 3.6 30.3 - - + -
540C PRO* 3.6 32.7 - - + +
543C LEU* 3.8 23.8 - - + -
547C VAL* 4.4 15.9 - - + -
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Residues in contact with GLY 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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510C LEU 3.2 7.6 + - - -
511C TYR* 2.9 9.5 + - - -
513C TRP* 1.3 78.4 - - - +
515C GLU* 1.3 61.2 + - - +
517C LEU* 3.7 10.9 + - - +
518C GLY* 3.4 14.7 + - - -
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Residues in contact with GLU 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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511C TYR* 3.2 25.0 + - + +
512C SER* 3.8 8.4 + - - +
513C TRP 3.2 0.4 - - - -
514C GLY* 1.3 77.4 - - - +
516C LEU* 1.3 59.3 + - + +
518C GLY* 3.2 3.6 + - - +
519C LYS* 3.1 26.7 + - - +
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Residues in contact with LEU 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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512C SER 3.1 13.9 + - - +
513C TRP* 3.3 16.8 + - + +
515C GLU* 1.3 74.5 - - + +
517C LEU* 1.3 59.3 + - - +
519C LYS* 3.4 6.4 + - + +
520C TRP* 3.0 59.3 + - + +
528C PRO* 3.6 38.4 - - + -
531C LEU* 3.9 18.6 - - + -
534C LEU* 3.5 32.5 - - + -
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Residues in contact with LEU 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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521A HIS 4.6 0.2 - - - -
524A LEU* 5.9 7.4 - - + -
513C TRP* 3.1 27.2 + - + +
514C GLY* 3.8 9.4 - - - +
516C LEU* 1.3 72.2 - - - +
518C GLY* 1.3 67.3 + - - +
520C TRP* 4.6 2.5 - - + -
521C HIS* 3.0 31.4 + - + +
543C LEU* 4.5 20.6 - - + -
546C GLU* 3.5 40.4 - - + +
547C VAL* 3.8 21.8 - - + -
550C LEU* 3.5 27.8 - - + +
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Residues in contact with GLY 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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521A HIS 3.2 25.8 + - - +
522A SER* 4.2 17.9 + - - -
514C GLY 3.4 8.0 + - - -
515C GLU* 3.2 8.2 + - - -
517C LEU* 1.3 80.7 - - - +
519C LYS* 1.3 62.0 + - - +
520C TRP 3.3 0.3 + - - -
521C HIS* 3.3 15.2 + - - +
522C SER* 3.8 5.7 + - - -
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Residues in contact with LYS 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 GLU 3.1 15.5 + - - +
516C LEU* 3.4 11.4 + - + +
518C GLY* 1.3 74.6 - - - +
520C TRP* 1.3 59.2 + - + +
522C SER* 3.2 7.4 + - - -
523C ASN* 2.9 30.9 + - - +
526C ALA* 4.6 15.7 - - + -
528C PRO* 5.6 3.1 - - + -
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Residues in contact with TRP 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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513C TRP* 4.2 13.9 - + - -
516C LEU* 3.0 44.1 + - + +
517C LEU* 4.4 1.6 - - + -
518C GLY 3.3 0.4 - - - -
519C LYS* 1.3 73.5 - - + +
521C HIS* 1.3 63.7 + - - +
522C SER 3.2 0.4 + - - -
523C ASN 3.5 16.8 - - - -
524C LEU* 3.5 23.1 + - - +
526C ALA* 2.7 30.4 + - + +
527C ARG* 3.6 9.3 - - - +
528C PRO* 4.9 1.6 - - - +
531C LEU* 3.8 39.0 - - + -
535C VAL* 5.2 2.7 - - + -
547C VAL* 3.7 31.2 - - + -
550C LEU* 3.8 39.0 - - + +
551C LEU* 3.8 25.4 - - + -
722C CYS* 5.0 0.7 - - - -
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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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521A HIS* 3.3 65.0 + + + +
524A LEU* 5.3 5.6 - - + -
546A GLU* 5.1 1.3 - - - -
517C LEU* 3.0 24.9 + - + -
518C GLY 3.3 9.3 + - - +
520C TRP* 1.3 77.9 - - - +
522C SER* 1.3 58.0 + - - +
546C GLU* 4.4 18.9 - - + +
550C LEU* 3.6 25.7 - - + +
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Residues in contact with SER 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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518A GLY* 6.1 3.6 - - - -
522A SER* 6.0 1.3 - - - -
518C GLY 3.8 5.3 + - - -
519C LYS* 3.2 8.9 + - - -
520C TRP 4.3 0.2 - - - -
521C HIS* 1.3 78.4 - - - +
523C ASN* 1.3 63.4 + - - +
524C LEU 4.2 0.2 - - - -
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Residues in contact with ASN 523 (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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519C LYS 2.9 15.7 + - - +
520C TRP* 3.5 11.4 - - - -
521C HIS 3.6 0.4 - - - -
522C SER* 1.3 82.1 - - - +
524C LEU* 1.3 63.4 + - - +
525C GLY* 3.0 17.3 + - - -
526C ALA* 3.2 29.3 + - + +
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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