Contacts of the helix formed by residues 534 - 540 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333B PRO 3.4 13.2 - - - -
334B GLN* 3.8 9.0 + - - -
335B TYR* 5.3 0.7 - - - -
360B LYS* 4.3 12.7 - - - +
500B ALA* 6.2 0.4 - - - -
531B GLY* 3.1 20.1 + - - -
532B GLU 3.4 1.2 + - - -
533B PHE* 1.3 75.7 - - - +
535B GLU* 1.3 67.2 + - - -
536B GLU 3.3 2.0 - - - -
537B TRP* 3.0 17.0 + - - +
538B HIS* 3.4 4.2 + - - +
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Residues in contact with GLU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LYS* 4.8 11.7 + - - +
284B LYS* 5.6 3.5 + - - -
329B ASN* 4.2 22.5 + - - +
333B PRO* 3.0 25.7 + - + +
335B TYR* 5.1 4.7 + - + -
500B ALA* 4.2 9.3 - - - +
534B GLY* 1.3 71.4 - - - -
536B GLU* 1.3 58.0 + - - +
538B HIS* 3.0 36.5 + - - +
539B LYS* 2.8 58.0 + - - +
542B ARG* 5.1 0.3 - - - -
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Residues in contact with GLU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B PRO* 4.1 25.6 - - + +
528B ARG* 5.9 0.2 - - - -
533B PHE 5.0 4.0 - - - +
534B GLY 3.3 1.2 - - - -
535B GLU* 1.3 78.3 - - - +
537B TRP* 1.3 57.7 + - - +
539B LYS* 3.5 28.3 + - - +
540B GLY* 3.0 22.9 + - - -
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Residues in contact with TRP 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B THR* 3.9 13.5 - - + -
472B LYS 3.7 13.7 - - - -
473B ILE* 3.4 33.2 - - + -
474B PRO* 4.6 0.2 - - + -
526B SER 3.0 28.8 + - - -
527B ILE 3.4 10.1 + - - -
528B ARG* 3.6 23.6 - - + +
529B GLY 3.0 19.4 + - - -
530B GLY 3.4 13.5 - - - +
532B GLU* 3.3 26.0 + - - +
533B PHE* 3.6 52.4 + + + +
534B GLY 3.0 12.6 + - - +
536B GLU* 1.3 77.4 - - - +
538B HIS* 1.3 62.7 + - - +
540B GLY 3.3 6.4 + - - -
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Residues in contact with HIS 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B THR 5.6 1.1 - - - -
282B SER* 5.2 17.0 - - - -
283B LYS* 5.8 2.2 - - + +
499B PHE* 3.8 6.0 + - - -
500B ALA* 3.5 21.6 - - + +
529B GLY* 3.2 20.3 - - - -
530B GLY 3.1 16.0 + - - +
534B GLY 3.4 1.8 + - - +
535B GLU* 3.0 40.1 + - - +
537B TRP* 1.3 77.0 - - - +
539B LYS* 1.3 62.3 + - - +
541B GLY 3.0 20.1 + - - -
542B ARG* 3.4 22.8 - - - +
621B SER 5.6 0.4 - - - -
622B GLU* 2.7 32.6 + - - -
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Residues in contact with LYS 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LYS* 5.8 6.3 - - - +
535B GLU* 2.8 47.7 + - + +
536B GLU* 3.9 29.2 + - - +
538B HIS* 1.3 72.0 - - - +
540B GLY* 1.3 55.8 + - - +
541B GLY 3.2 0.4 - - - -
542B ARG* 3.5 38.9 + - - +
545B THR* 2.8 23.2 + - - +
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Residues in contact with GLY 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B ARG* 3.8 21.0 - - - +
536B GLU 3.0 16.1 + - - -
537B TRP 3.3 4.0 + - - -
538B HIS 3.1 1.6 - - - -
539B LYS* 1.3 76.2 - - - +
541B GLY* 1.3 53.9 + - - +
545B THR* 3.3 7.4 - - - -
548B ASN* 2.9 34.3 + - - +
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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