Contacts of the strand formed by residues 3587 - 3593 (chain J) in PDB entry 2ZLE
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 ALA3587 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3535J VAL* 3.3 25.8 - - + -
3536J GLU 3.7 5.2 - - - +
3537J GLY* 4.3 0.7 - - - -
3584J VAL* 2.9 20.6 + - + +
3585J ASP 3.1 0.8 - - - -
3586J ASN* 1.3 80.3 - - - +
3588J THR* 1.3 61.7 + - - +
3589J VAL 4.4 0.2 - - - +
3590J ILE* 4.0 23.1 - - + -
3604J MET* 5.5 6.8 - - + +
3831J VAL* 5.7 5.0 - - - +
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Residues in contact with THR3588 (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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3536J GLU* 2.8 11.2 + - - +
3537J GLY* 3.4 15.0 - - - -
3538J SER* 3.7 10.9 + - - -
3586J ASN 4.2 0.9 + - - -
3587J ALA* 1.3 75.5 + - - +
3589J VAL* 1.3 73.4 + - + +
3590J ILE* 4.3 1.7 - - - +
3831J VAL* 6.5 1.3 - - - -
3837J PHE* 5.0 20.1 - - + -
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Residues in contact with VAL3589 (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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3534J ASN 3.8 1.1 - - - +
3535J VAL* 3.4 2.6 - - - +
3536J GLU* 2.8 64.8 + - + +
3588J THR* 1.3 91.5 - - + +
3590J ILE* 1.3 65.5 - - - +
3591J LYS* 4.1 29.6 - - + -
3601J ASP* 5.6 1.6 - - - +
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Residues in contact with ILE3590 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3533J ILE* 3.6 20.9 - - + -
3534J ASN 3.6 2.5 - - - -
3535J VAL* 4.3 10.5 - - + -
3584J VAL* 5.1 6.7 - - + -
3587J ALA* 4.0 18.4 - - + -
3588J THR 5.4 1.3 - - - +
3589J VAL* 1.3 78.8 - - - +
3591J LYS* 1.3 75.8 + - - +
3592J VAL* 3.7 6.1 - - + -
3601J ASP* 4.0 2.1 - - - +
3602J ALA* 2.9 50.6 + - + +
3603J LYS* 4.7 5.6 - - - +
3604J MET* 5.0 10.8 - - + +
3616J ILE* 3.6 26.9 - - + -
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Residues in contact with LYS3591 (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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3533J ILE* 3.3 4.5 - - - -
3534J ASN* 2.7 52.2 + - + +
3536J GLU* 5.9 1.3 + - - -
3589J VAL* 4.1 21.7 - - + -
3590J ILE* 1.3 78.0 - - - +
3592J VAL* 1.3 62.0 + - - +
3599J LYS* 5.3 20.4 - - - +
3600J PHE 3.8 5.6 - - - +
3601J ASP* 3.8 24.7 - - - +
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Residues in contact with VAL3592 (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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3531J VAL* 3.5 33.4 - - + -
3532J SER 3.4 5.2 - - - +
3533J ILE* 4.2 4.0 - - + -
3577J VAL* 5.5 0.7 - - + -
3590J ILE* 3.7 17.5 - - + -
3591J LYS* 1.3 80.5 - - - +
3593J GLN* 1.3 65.0 + - - +
3594J LEU* 4.3 3.8 + - + +
3598J ARG 4.1 0.2 - - - +
3599J LYS* 3.5 4.3 - - - +
3600J PHE* 2.8 44.4 + - + +
3602J ALA* 3.9 9.0 - - + -
3616J ILE* 3.8 16.4 - - + -
3618J ILE* 4.5 23.1 - - + -
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Residues in contact with GLN3593 (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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3531J VAL* 3.7 0.5 - - - -
3532J SER* 3.1 45.9 + - - +
3592J VAL* 1.3 77.7 - - - +
3594J LEU* 1.3 72.8 + - - +
3597J GLY* 3.3 22.4 - - - +
3598J ARG 3.4 11.2 - - - +
3599J LYS* 3.9 25.5 - - + +
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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