Contacts of the helix formed by residues 540 - 551 (chain B) 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 PRO 540 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534B LEU 5.6 0.7 - - - +
538B GLY 3.3 9.8 - - - +
539B VAL* 1.4 88.3 - - + +
541B GLU* 1.3 59.7 + - - +
542B ALA* 3.4 1.6 - - + +
543B LEU* 2.9 36.3 + - + +
544B ARG 2.9 25.5 + - - -
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Residues in contact with GLU 541 (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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539B VAL 3.6 1.4 + - - -
540B PRO* 1.3 70.0 - - - +
542B ALA* 1.3 59.3 + - - +
544B ARG* 2.9 54.2 + - - +
545B ALA* 4.4 1.7 + - - +
633B HIS* 2.7 38.8 + - + +
714B PHE* 3.8 12.4 - - - -
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Residues in contact with ALA 542 (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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540B PRO* 3.4 1.9 - - + +
541B GLU* 1.3 78.4 - - - +
543B LEU* 1.3 63.7 + - + +
544B ARG 3.5 0.2 - - - -
545B ALA* 4.5 11.0 + - - +
546B GLU* 5.2 0.9 + - - +
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Residues in contact with LEU 543 (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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539B VAL* 4.0 8.1 - - + -
540B PRO* 2.9 37.9 + - + +
542B ALA* 1.3 80.3 - - + +
544B ARG* 1.3 57.1 + - - +
545B ALA 3.3 2.9 + - - -
546B GLU* 3.6 10.3 + - + +
547B VAL* 2.9 33.8 + - + +
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Residues in contact with ARG 544 (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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539B VAL* 3.2 29.6 + - + +
540B PRO 2.9 18.0 + - - +
541B GLU* 2.9 42.0 + - - +
543B LEU* 1.3 77.3 - - - +
545B ALA* 1.3 57.0 + - - +
548B TRP* 2.7 53.6 + - + +
633B HIS* 3.6 31.9 - - + +
711B CYS 5.4 1.0 + - - -
714B PHE* 3.6 29.1 + - - +
715B HIS* 3.9 22.2 + - - +
718B ASP* 2.7 35.1 + - - +
766B GLU* 5.5 4.0 + - - -
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Residues in contact with ALA 545 (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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541B GLU 4.4 2.0 + - - -
542B ALA 4.6 10.5 - - - +
544B ARG* 1.3 81.1 - - - +
546B GLU* 1.3 61.8 + - - +
549B GLN* 3.3 32.4 + - - +
633B HIS* 3.2 27.8 + - - +
634B MSE 3.7 14.2 - - + +
635B PRO* 5.8 2.0 - - + -
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Residues in contact with GLU 546 (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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542B ALA 5.2 0.6 + - - +
543B LEU* 3.6 11.3 + - + +
544B ARG 3.5 0.2 - - - -
545B ALA* 1.3 79.0 - - + +
547B VAL* 1.3 62.4 + - - +
549B GLN* 3.5 7.5 + - - +
550B LEU* 3.1 38.7 + - + +
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Residues in contact with VAL 547 (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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539B VAL* 3.6 29.4 - - + -
543B LEU* 2.9 22.9 + - + +
544B ARG 3.9 0.2 - - - +
546B GLU* 1.3 77.6 - - - +
548B TRP* 1.3 63.9 + - + +
550B LEU* 3.6 10.1 - - - +
551B LEU* 3.2 31.4 + - + +
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Residues in contact with TRP 548 (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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539B VAL* 5.1 1.6 - - + -
544B ARG* 2.7 47.6 + - + +
547B VAL* 1.3 73.5 - - + +
549B GLN* 1.3 66.9 + - - +
551B LEU* 3.1 24.2 + - + +
629B VAL* 3.9 15.7 - - + -
630B LEU* 3.3 41.1 - - + -
633B HIS* 3.3 29.8 - + + -
634B MSE 3.7 22.4 - - + -
642B VAL* 5.9 3.4 - - + -
714B PHE* 3.9 8.1 - + - -
717B ILE* 3.6 24.5 - - + -
718B ASP* 2.6 30.3 + - - +
721B LEU* 3.6 29.1 - - + +
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Residues in contact with GLN 549 (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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545B ALA* 3.3 24.8 + - - +
546B GLU* 3.5 5.7 + - - +
548B TRP* 1.3 75.7 - - - +
550B LEU* 1.3 66.9 + - - +
551B LEU 3.1 7.1 + - - -
634B MSE 3.8 24.0 - - + +
638B GLN* 2.8 44.8 + - - +
641B CYS* 6.0 1.4 - - - +
642B VAL* 5.2 9.6 - - + -
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Residues in contact with LEU 550 (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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546B GLU* 3.1 31.9 + - + +
547B VAL* 3.6 9.4 - - - +
549B GLN* 1.3 78.5 - - - +
551B LEU* 1.3 62.1 + - + +
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Residues in contact with LEU 551 (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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535B VAL* 4.6 15.0 - - + -
539B VAL* 5.5 2.7 - - + -
547B VAL* 3.2 20.1 + - + +
548B TRP* 3.1 19.2 + - + +
549B GLN 3.5 9.2 - - - -
550B LEU* 1.3 85.2 - - + +
650B TYR* 2.9 25.5 + - - -
718B ASP* 4.1 20.6 - - - +
721B LEU* 4.1 20.6 - - + +
722B CYS* 4.3 27.1 - - + +
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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