Contacts of the helix formed by residues 534 - 539 (chain E) in PDB entry 4E2I
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 534 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491E ILE* 3.5 28.0 - - + +
495E ASP* 4.5 3.4 - - + +
532E SER* 4.0 2.0 - - - +
533E VAL* 1.3 87.2 - - - +
535E LYS* 1.3 60.0 + - - +
536E THR* 4.0 10.3 - - - +
537E LEU* 3.0 15.9 + - + +
538E GLN* 2.9 25.5 + - - +
484F ASP* 4.9 3.4 - - + +
486F PRO* 3.7 34.1 - - + -
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Residues in contact with LYS 535 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533E VAL 3.7 1.4 + - - -
534E PRO* 1.3 72.9 - - - +
536E THR* 1.3 79.1 + - + +
537E LEU 3.0 0.4 - - - -
538E GLN* 4.0 7.4 - - - +
539E ALA* 3.1 26.2 + - - +
428F ILE* 3.9 24.2 - - + +
483F ARG* 3.7 24.9 + - - +
484F ASP* 4.4 20.1 + - + +
485F LEU* 4.6 5.6 - - - +
530F GLU* 5.7 3.0 + - - -
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Residues in contact with THR 536 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495E ASP* 2.9 26.3 + - - -
498E ARG* 2.9 22.4 + - - +
534E PRO* 4.0 1.6 - - - +
535E LYS* 1.3 85.2 - - + +
537E LEU* 1.3 56.4 + - - +
539E ALA* 4.2 2.3 + - - +
540E ARG* 3.0 30.1 + - - +
428F ILE* 3.4 30.9 - - + +
484F ASP 4.7 2.9 - - - +
485F LEU* 3.7 29.2 - - + -
486F PRO* 4.0 7.6 - - + +
529F ASN* 4.3 1.8 - - - +
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Residues in contact with LEU 537 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491E ILE* 3.8 20.9 - - + +
494E LEU* 3.6 42.8 - - + -
495E ASP* 4.2 8.5 - - + +
498E ARG* 5.3 0.7 - - - +
501E LEU* 3.8 19.5 - - + -
528E MET* 5.3 0.7 - - + -
533E VAL* 3.5 19.3 - - + -
534E PRO* 3.0 27.3 + - + +
535E LYS 3.0 0.4 - - - -
536E THR* 1.3 79.5 + - - +
538E GLN* 1.3 61.0 + - - +
539E ALA 3.0 1.6 - - - -
540E ARG* 2.9 23.7 + - + +
541E PHE* 3.1 28.0 - - + -
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Residues in contact with GLN 538 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E LEU* 3.8 26.2 - - - +
425E LYS* 5.7 0.5 + - - -
533E VAL* 3.6 25.7 - - + +
534E PRO 2.9 15.1 + - - +
535E LYS* 3.5 8.3 + - - +
537E LEU* 1.3 75.9 - - - +
539E ALA* 1.3 57.2 + - - +
540E ARG 3.0 4.4 + - - -
541E PHE* 3.1 36.3 + - - +
543E LYS 5.7 0.4 - - - -
544E GLN* 3.9 25.4 + - - +
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Residues in contact with ALA 539 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418E LYS* 3.5 26.9 - - - +
535E LYS 3.1 17.1 + - - +
536E THR 4.3 7.6 - - - +
537E LEU 3.0 1.2 - - - -
538E GLN* 1.3 75.6 - - - +
540E ARG* 1.3 59.3 + - - +
541E PHE 3.4 3.1 - - - +
428F ILE* 4.1 14.1 - - + -
429F ASP* 3.3 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