Contacts of the strand formed by residues 3613 - 3619 (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 ILE3613 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3578J VAL* 4.2 16.2 - - + -
3579J THR 3.5 2.2 - - - +
3581J ASN* 4.0 2.1 - - - +
3608J ASP 3.0 26.1 + - - +
3611J SER* 3.3 30.2 + - - +
3612J ASP* 1.3 77.4 - - - +
3614J ALA* 1.3 65.8 + - - +
3693J ILE* 3.8 32.5 - - + -
3695J THR* 6.4 0.2 - - - -
3711J ILE* 3.7 25.1 - - + -
3716J VAL* 4.3 17.0 - - + +
3719J LEU* 4.2 15.9 - - + -
3720J THR* 5.3 3.8 - - - +
3723J MET* 3.4 12.2 - - + +
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Residues in contact with ALA3614 (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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3578J VAL* 3.5 6.3 - - - +
3579J THR* 2.6 47.9 + - + +
3580J ASN 4.2 1.3 - - - +
3581J ASN* 3.9 8.1 - - - -
3584J VAL* 3.7 29.2 - - + -
3606J GLY 3.5 13.2 - - - +
3607J LYS* 3.9 8.1 - - + +
3613J ILE* 1.3 77.0 - - - +
3615J LEU* 1.3 61.0 + - - +
3720J THR* 5.6 0.2 - - - -
3723J MET* 4.3 2.9 - - - -
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Residues in contact with LEU3615 (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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3570J ILE* 5.1 4.5 - - + -
3576J TYR* 4.2 16.2 - - + -
3577J VAL 3.0 36.6 - - - +
3578J VAL* 3.8 7.2 - - + +
3604J MET* 4.0 0.3 - - - +
3605J VAL* 3.1 37.6 + - + +
3606J GLY 2.8 13.8 + - - +
3614J ALA* 1.3 72.7 - - - +
3616J ILE* 1.3 74.5 + - - +
3720J THR* 3.3 30.1 - - + +
3723J MET* 3.7 16.9 - - + -
3724J VAL* 3.9 27.8 - - + -
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Residues in contact with ILE3616 (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* 3.9 17.9 - - + -
3576J TYR* 3.4 6.8 - - - -
3577J VAL* 2.8 51.1 + - + +
3579J THR* 4.4 5.4 - - + -
3584J VAL* 4.3 20.4 - - + -
3590J ILE* 3.6 32.1 - - + -
3592J VAL* 3.8 11.9 - - + -
3602J ALA* 3.8 11.0 - - + -
3603J LYS 3.4 15.0 - - - +
3604J MET* 4.4 13.2 - - + +
3605J VAL* 3.4 5.6 - - - -
3615J LEU* 1.3 85.3 - - - +
3617J GLN* 1.3 63.2 + - - +
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Residues in contact with GLN3617 (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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3574J LYS* 2.9 39.7 - - - +
3575J GLY 3.1 1.1 - - - +
3576J TYR* 3.4 34.4 + - + -
3602J ALA* 3.2 5.2 - - - -
3603J LYS* 3.0 35.0 + - + +
3605J VAL* 4.5 7.0 - - + +
3616J ILE* 1.3 75.0 - - - +
3618J ILE* 1.3 69.5 + - - +
3619J GLN* 3.2 13.4 + - - +
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Residues in contact with ILE3618 (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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3569J ILE* 4.6 5.2 - - + -
3574J LYS 4.4 1.4 - - - +
3575J GLY* 2.7 21.8 + - - +
3577J VAL* 3.9 26.9 - - + -
3592J VAL* 4.5 22.2 - - + -
3594J LEU* 4.6 8.3 - - + -
3600J PHE* 3.4 44.0 - - + -
3601J ASP 3.4 4.7 - - - -
3602J ALA* 4.3 1.6 - - + -
3616J ILE* 5.9 0.2 - - + -
3617J GLN* 1.3 81.2 - - - +
3619J GLN* 1.3 65.8 + - - +
3620J ASN 3.4 2.9 + - - -
3621J PRO* 3.6 18.1 - - + +
3624J LEU* 3.6 28.7 - - + -
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Residues in contact with GLN3619 (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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3600J PHE* 3.9 6.4 - - - -
3601J ASP* 2.5 38.5 + - + +
3603J LYS* 3.2 46.2 - - + +
3617J GLN* 3.3 27.1 + - - +
3618J ILE* 1.3 78.1 - - - +
3620J ASN* 1.3 80.7 + - - +
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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