Contacts of the helix formed by residues 534 - 539 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491J ILE* 3.5 27.6 - - + +
495J ASP* 4.5 3.4 - - + +
532J SER* 4.0 2.0 - - - +
533J VAL* 1.3 87.6 - - - +
535J LYS* 1.3 59.8 + - - +
536J THR* 4.0 7.2 - - - +
537J LEU* 3.0 16.2 + - + +
538J GLN* 2.9 24.8 + - - +
484K ASP 5.4 1.3 - - - +
486K PRO* 3.8 30.5 - - + -
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Residues in contact with LYS 535 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533J VAL 3.7 1.9 + - - -
534J PRO* 1.3 72.7 - - - +
536J THR* 1.3 72.8 + - + +
537J LEU 3.0 0.2 - - - -
538J GLN* 4.0 6.8 - - - +
539J ALA* 3.1 26.7 + - - +
428K ILE* 4.7 20.1 - - + +
483K ARG* 3.4 27.4 + - - +
484K ASP* 3.7 32.4 + - + +
485K LEU* 4.7 3.8 - - - +
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Residues in contact with THR 536 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495J ASP* 2.9 26.0 + - - -
498J ARG* 2.9 23.7 + - - +
534J PRO* 4.0 0.9 - - - +
535J LYS* 1.3 89.4 - - + +
537J LEU* 1.3 57.5 + - - +
539J ALA* 4.2 2.6 + - - +
540J ARG* 3.0 30.5 + - - +
428K ILE* 4.1 24.5 - - + -
484K ASP 4.1 0.2 - - - +
485K LEU* 3.9 28.0 - - + -
486K PRO* 3.5 15.1 - - + +
529K ASN* 5.0 1.3 - - - +
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Residues in contact with LEU 537 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491J ILE* 3.8 21.1 - - + +
494J LEU* 3.6 41.7 - - + -
495J ASP* 4.2 9.2 - - + +
498J ARG* 5.3 1.1 - - - +
501J LEU* 3.8 20.4 - - + -
528J MET* 5.3 0.4 - - + -
533J VAL* 3.5 19.5 - - + -
534J PRO* 3.0 26.4 + - + +
535J LYS 3.0 0.4 - - - -
536J THR* 1.3 80.6 + - - +
538J GLN* 1.3 61.0 + - - +
539J ALA 3.0 1.6 - - - -
540J ARG* 2.9 23.8 + - - +
541J PHE* 3.1 27.4 - - + -
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Residues in contact with GLN 538 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423J LEU* 3.8 26.6 - - - +
425J LYS* 5.7 0.2 + - - -
533J VAL* 3.6 24.5 - - + +
534J PRO 2.9 15.0 + - - +
535J LYS* 3.4 8.7 + - - +
537J LEU* 1.3 77.5 - - - +
539J ALA* 1.3 56.0 + - - +
540J ARG 3.0 4.8 + - - -
541J PHE* 3.1 36.6 + - - +
543J LYS 5.7 0.6 - - - -
544J GLN* 3.9 24.8 + - - +
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Residues in contact with ALA 539 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418J LYS* 3.5 28.7 - - - +
535J LYS 3.1 17.9 + - - +
536J THR* 4.4 7.9 - - - +
537J LEU 3.0 0.8 - - - -
538J GLN* 1.3 76.5 - - - +
540J ARG* 1.3 59.5 + - - +
541J PHE 3.4 2.9 - - - +
428K ILE* 4.3 15.3 - - + -
429K ASP* 4.0 19.7 - - - +
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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