Contacts of the helix formed by residues 534 - 540 (chain A) in PDB entry 5N4D
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 GLY 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A PRO 3.4 13.7 - - - -
334A GLN* 3.6 9.2 + - - -
335A TYR* 5.4 0.4 - - - -
360A LYS* 4.4 12.0 - - - +
500A ALA* 6.3 0.4 - - - -
531A GLY* 3.0 20.9 + - - +
532A GLU 3.4 1.4 + - - -
533A PHE* 1.3 75.7 - - - +
535A GLU* 1.3 61.0 + - - -
536A GLU 3.2 2.0 - - - -
537A TRP* 2.9 24.1 + - - +
538A HIS 3.4 3.6 + - - -
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Residues in contact with GLU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LYS* 4.6 14.8 - - - +
284A LYS* 5.5 3.0 + - - -
329A ASN* 4.2 21.5 + - - +
333A PRO* 2.9 26.0 + - + +
335A TYR* 5.1 5.0 + - + -
500A ALA* 4.1 10.8 - - - +
534A GLY* 1.3 72.7 - - - -
536A GLU* 1.3 57.9 + - - +
538A HIS* 2.8 37.4 + - - +
539A LYS* 2.8 63.9 + - - +
542A ARG* 5.7 0.2 + - - -
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Residues in contact with GLU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A PRO* 4.0 25.7 - - + +
533A PHE 4.5 4.7 + - - +
534A GLY 3.2 1.0 - - - -
535A GLU* 1.3 74.6 - - - +
537A TRP* 1.3 62.0 + - - +
539A LYS* 3.8 25.0 + - - +
540A GLY* 3.0 23.7 + - - -
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Residues in contact with TRP 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A THR* 4.0 12.3 - - + -
472A LYS 3.9 12.3 - - - -
473A ILE* 3.4 32.5 - - + -
474A PRO* 4.6 0.4 - - + -
526A SER 3.0 29.3 + - - -
527A ILE 3.4 10.6 + - - -
528A ARG* 3.6 23.6 - - + +
529A GLY 3.0 19.8 + - - -
530A GLY 3.4 13.7 - - - +
532A GLU* 3.4 25.5 + - - -
533A PHE* 3.6 51.1 + + + +
534A GLY 2.9 11.2 + - - +
536A GLU* 1.3 79.4 - - - +
538A HIS* 1.3 60.9 + - - +
540A GLY* 3.4 9.7 + - - -
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Residues in contact with HIS 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A THR 5.6 1.6 - - - -
282A SER* 5.3 15.9 - - - -
283A LYS* 5.7 2.7 - - + -
499A PHE* 3.8 6.2 + - - -
500A ALA* 3.5 20.7 - - + +
529A GLY* 3.2 19.9 - - - -
530A GLY 3.1 17.4 + - - +
534A GLY 3.4 2.2 + - - +
535A GLU* 2.8 42.6 + - - +
537A TRP* 1.3 78.3 - - - +
539A LYS* 1.4 56.6 + - - +
541A GLY 3.0 20.6 + - - -
542A ARG* 3.4 21.7 - - + +
621A SER 5.6 1.6 - - - -
622A GLU* 2.8 33.1 + - - -
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Residues in contact with LYS 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LYS* 5.3 11.5 - - - +
535A GLU* 2.8 58.9 + - - +
536A GLU* 3.9 28.4 + - - +
538A HIS* 1.4 71.2 - - - +
540A GLY* 1.3 51.3 + - - +
541A GLY 3.2 0.4 - - - -
542A ARG* 3.5 43.6 + - - +
545A THR* 2.8 26.2 + - - +
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Residues in contact with GLY 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A ARG* 3.7 20.9 - - - +
536A GLU 3.0 14.0 + - - -
537A TRP 3.4 6.0 + - - -
538A HIS 3.1 1.2 - - - -
539A LYS* 1.3 76.4 - - - +
541A GLY* 1.3 54.7 + - - +
545A THR* 3.3 6.5 - - - +
548A ASN* 2.8 35.5 + - - +
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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