Contacts of the helix formed by residues 514 - 523 (chain D) in PDB entry 2ZXI
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 514 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509D MET* 4.1 3.1 - - - -
512D ASN 5.4 2.0 - - - +
513D TYR* 1.3 77.9 - - - +
515D LEU* 1.3 66.2 + - - +
516D ASP* 3.5 9.8 + - - +
517D ASP* 2.7 49.7 + - - +
518D VAL* 3.1 15.4 + - - +
537D GLU* 3.5 23.3 - - - +
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Residues in contact with LEU 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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487D TYR* 3.6 45.5 - - + +
505D VAL* 4.6 5.4 - - + -
509D MET* 3.3 29.8 - - + +
514D THR* 1.3 71.3 - - - +
516D ASP* 1.3 61.9 + - - +
518D VAL* 3.1 7.3 + - + +
519D LYS* 2.9 24.3 + - - +
526D VAL* 3.9 9.0 - - + +
527D PRO* 4.2 8.5 - - + -
533D LYS* 3.4 44.6 - - + +
536D VAL* 4.2 3.6 - - + -
537D GLU* 2.7 26.8 + - + +
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Residues in contact with ASP 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514D THR* 3.1 9.9 + - - +
515D LEU* 1.3 77.3 - - - +
517D ASP* 1.3 61.0 + - - +
519D LYS* 3.5 9.7 + - - +
520D GLU* 3.0 25.6 + - - +
526D VAL* 5.2 2.3 - - - +
533D LYS* 2.7 32.9 + - - -
537D GLU* 4.3 1.2 + - - -
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Residues in contact with ASP 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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512D ASN 3.9 5.5 - - - +
513D TYR* 3.6 24.5 - - + -
514D THR* 2.7 51.2 + - - +
516D ASP* 1.3 76.7 - - - +
518D VAL* 1.3 57.8 + - - +
520D GLU* 3.2 4.9 + - - +
521D LYS* 2.8 34.5 + - - +
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Residues in contact with VAL 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D TYR* 5.6 1.1 - - + -
505D VAL* 4.1 29.8 - - + -
508D LEU* 4.4 8.3 - - + -
509D MET* 4.7 4.0 - - - -
513D TYR* 4.0 23.6 - - + -
514D THR 3.2 15.9 - - - +
515D LEU* 3.1 11.8 + - + +
517D ASP* 1.3 77.0 - - - +
519D LYS* 1.3 56.7 + - - +
522D PHE* 2.9 42.7 + - + +
523D GLY 3.3 1.7 + - - -
524D TYR* 3.7 27.6 + - + -
526D VAL* 6.2 0.2 - - + -
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Residues in contact with LYS 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 LEU 2.9 14.1 + - - +
516D ASP* 3.9 9.2 - - - +
518D VAL* 1.3 75.6 - - - +
520D GLU* 1.3 61.1 + - - +
523D GLY* 2.9 26.4 + - - -
524D TYR 3.0 30.7 + - - +
525D GLU* 3.9 21.8 + - - +
526D VAL* 4.0 27.8 - - + +
528D GLN* 5.3 3.5 - - - +
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Residues in contact with GLU 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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516D ASP 3.0 18.7 + - - +
517D ASP* 3.5 6.7 - - - +
519D LYS* 1.3 79.6 - - - +
521D LYS* 1.3 63.2 + - + +
523D GLY 4.5 0.5 + - - -
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Residues in contact with LYS 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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513D TYR* 3.4 24.7 + - + +
517D ASP 2.8 20.1 + - - +
520D GLU* 1.3 78.3 - - + +
522D PHE* 1.3 95.4 + - + +
523D GLY 3.5 0.2 - - - -
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Residues in contact with PHE 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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492D VAL* 3.2 31.6 - - + -
493D SER 4.7 4.3 - - - -
494D VAL* 3.9 19.7 - - + -
508D LEU* 3.7 22.2 - - + -
513D TYR* 3.9 12.8 - + - -
518D VAL* 2.9 32.5 + - + +
521D LYS* 1.3 105.8 - - + +
523D GLY* 1.3 62.3 + - - +
524D TYR* 3.3 24.0 + + + -
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Residues in contact with GLY 523 (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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518D VAL 3.3 0.4 + - - -
519D LYS* 2.9 21.2 + - - -
520D GLU 4.5 0.8 + - - -
521D LYS 3.5 2.2 + - - -
522D PHE* 1.3 77.4 - - - +
524D TYR* 1.3 65.9 + - - +
525D GLU* 4.0 1.7 + - - +
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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