Contacts of the helix formed by residues 551 - 559 (chain D) in PDB entry 2VKX
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 ASP 551 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532C LYS* 5.6 3.3 + - - -
551C ASP* 5.5 10.0 - - + +
554C GLU* 2.9 20.5 + - - +
531D LEU* 5.9 0.3 - - - -
532D LYS* 3.4 31.5 + - - +
550D TYR* 1.3 68.9 - - - +
552D ALA* 1.3 65.0 + - - +
553D LYS* 3.0 20.9 + - - +
554D GLU* 2.9 29.4 + - + +
555D ALA* 2.9 23.2 + - - +
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Residues in contact with ALA 552 (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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530D ILE* 2.9 41.5 - - + +
531D LEU* 3.6 2.5 - - - -
532D LYS* 3.0 22.6 - - - +
533D TYR* 3.7 17.2 - - + -
550D TYR 3.1 6.3 + - - -
551D ASP* 1.3 72.4 + - - +
553D LYS* 1.3 55.6 + - - +
555D ALA* 3.9 0.2 - - - +
556D SER* 2.5 40.0 + - - +
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Residues in contact with LYS 553 (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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530D ILE 5.3 5.1 + - - -
551D ASP* 3.1 17.4 + - - +
552D ALA* 1.3 82.7 - - - +
554D GLU* 1.3 64.8 + - - +
556D SER* 3.5 5.3 + - - -
557D MET* 3.2 36.2 + - + +
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Residues in contact with GLU 554 (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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532C LYS* 5.6 0.3 + - - -
548C LYS* 4.1 18.7 + - - +
549C TRP 4.5 2.4 - - - +
550C TYR* 3.8 19.7 - - - +
551C ASP* 3.4 29.4 + - + +
554C GLU* 2.5 36.9 - - - +
558C GLU* 5.1 0.3 - - - +
551D ASP* 2.9 26.2 + - + +
553D LYS* 1.3 77.5 - - - +
555D ALA* 1.3 62.8 + - - +
557D MET* 3.5 22.5 + - - +
558D GLU* 3.6 17.0 + - - +
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Residues in contact with ALA 555 (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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554C GLU* 5.6 1.3 + - - +
519D PHE* 4.1 5.6 - - + -
533D TYR* 3.9 20.6 - - + -
550D TYR* 4.8 4.3 - - + -
551D ASP 2.9 16.0 + - - +
552D ALA 3.9 2.7 - - - +
554D GLU* 1.3 77.0 + - - +
556D SER* 1.3 56.0 + - - +
557D MET 3.2 0.3 + - - -
558D GLU* 3.3 2.3 + - - -
559D GLY* 2.5 37.2 + - - -
560D ILE 3.7 10.0 + - - +
561D VAL* 4.0 22.4 - - + -
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Residues in contact with SER 556 (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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519D PHE* 5.4 1.6 - - - -
521D GLU* 2.9 35.9 + - - +
530D ILE* 5.4 1.4 - - - +
533D TYR* 4.1 10.8 + - - -
552D ALA* 2.5 32.5 + - - +
553D LYS* 3.2 6.9 + - - -
555D ALA* 1.3 73.1 - - - +
557D MET* 1.3 66.2 + - - +
559D GLY* 3.5 8.2 + - - +
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Residues in contact with MET 557 (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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548C LYS* 3.8 24.5 - - - +
553D LYS* 3.2 26.2 + - + +
554D GLU* 3.5 10.3 - - - +
555D ALA 3.1 0.8 - - - -
556D SER* 1.3 81.9 - - - +
558D GLU* 1.3 63.1 + - + +
559D GLY* 3.3 0.5 + - - -
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Residues in contact with GLU 558 (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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548C LYS* 3.6 30.4 - - + +
550C TYR* 4.1 3.0 + - - -
562C THR* 2.9 29.9 - - - +
564C VAL* 4.1 31.0 + - + +
554D GLU* 3.6 19.4 + - - +
555D ALA* 3.3 4.6 + - - +
557D MET* 1.3 79.6 - - + +
559D GLY* 1.3 61.6 + - - +
560D ILE* 3.3 33.6 + - + +
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Residues in contact with GLY 559 (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 GLN* 3.6 4.8 - - - +
519D PHE* 3.2 38.7 + - - +
555D ALA 2.5 18.2 + - - -
556D SER* 4.1 7.4 - - - -
557D MET 3.2 3.4 - - - -
558D GLU* 1.3 72.6 - - - +
560D ILE* 1.3 63.5 + - - +
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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