Contacts of the helix formed by residues 3519 - 3527 (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 LEU3519 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2846H GLY* 2.8 23.0 + - - +
2848H TYR* 3.7 23.1 - - + +
2866H ILE* 4.2 20.4 - - + -
3518J SER* 1.3 75.2 - - - +
3520J ALA* 1.3 59.5 + - - +
3521J PRO 3.3 1.6 - - - -
3522J MET* 3.2 18.2 + - + +
3523J LEU* 2.9 33.1 + - + +
3642J VAL* 4.9 13.2 - - + -
3656J SER* 4.0 27.4 - - - +
3686J LEU* 3.8 30.5 - - + -
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Residues in contact with ALA3520 (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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2844H ARG* 3.7 37.5 - - + +
2845H VAL 4.7 0.2 - - - +
2846H GLY* 3.1 21.4 - - - +
3518J SER* 3.0 13.6 + - - +
3519J LEU* 1.3 77.8 - - - +
3521J PRO* 1.3 67.8 - - + +
3523J LEU* 3.8 3.3 - - - +
3524J GLU* 3.0 31.6 + - + +
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Residues in contact with PRO3521 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2844H ARG* 4.0 17.0 - - - +
3518J SER* 3.3 25.1 - - - +
3520J ALA* 1.3 97.1 - - + +
3522J MET* 1.3 58.9 + - - +
3524J GLU* 3.7 12.8 + - + +
3525J LYS* 3.7 21.5 + - - +
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Residues in contact with MET3522 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3518J SER 5.3 0.2 + - - -
3519J LEU* 3.2 25.6 + - + +
3521J PRO* 1.3 75.5 - - - +
3523J LEU* 1.3 88.3 + - + +
3524J GLU 3.1 2.0 - - - -
3525J LYS* 2.8 29.0 + - - +
3526J VAL* 3.0 34.6 + - - +
3642J VAL* 3.2 37.2 - - + -
3684J VAL* 3.7 0.9 - - + -
3685J ASN 3.7 12.6 - - - +
3686J LEU* 4.0 22.0 - - + +
3687J ASN 5.0 2.7 - - - +
3688J GLY* 3.8 12.6 - - - +
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Residues in contact with LEU3523 (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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2845H VAL* 3.7 19.3 - - + -
2846H GLY* 3.4 33.7 - - - +
3519J LEU* 2.9 21.0 + - + +
3520J ALA* 3.8 5.4 - - - +
3522J MET* 1.3 102.6 - - + +
3524J GLU* 1.3 57.9 + - + +
3526J VAL* 2.9 3.3 + - + -
3527J MET* 2.8 43.5 + - + +
3642J VAL* 4.3 13.2 - - + -
3644J ILE* 4.5 17.0 - - + -
3654J VAL* 3.8 17.7 - - + -
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Residues in contact with GLU3524 (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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2844H ARG* 2.6 42.6 + - - -
3520J ALA* 3.0 18.7 + - + +
3521J PRO* 4.0 8.8 - - - +
3522J MET 3.1 0.6 - - - -
3523J LEU* 1.3 77.3 - - + +
3525J LYS* 1.3 60.2 + - + +
3527J MET* 4.9 3.1 - - - +
3528J PRO* 3.5 18.4 - - - +
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Residues in contact with LYS3525 (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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3521J PRO 3.7 17.9 - - - +
3522J MET* 2.8 18.5 + - - +
3524J GLU* 1.3 79.6 - - + +
3526J VAL* 1.3 63.4 + - + +
3528J PRO* 4.0 5.6 - - - +
3529J SER* 5.1 3.5 + - - -
3625J THR* 5.5 5.2 - - - +
3687J ASN 4.8 11.9 + - - -
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Residues in contact with VAL3526 (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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3522J MET* 3.0 23.1 + - - +
3523J LEU* 2.9 8.1 + - + +
3525J LYS* 1.3 81.8 - - + +
3527J MET* 1.3 69.8 + - - +
3528J PRO* 3.2 3.6 - - - -
3529J SER* 2.7 22.9 + - - -
3530J VAL* 3.9 5.8 + - + -
3627J ILE* 4.1 19.3 - - + -
3644J ILE* 3.7 28.0 - - + -
3684J VAL* 4.5 4.3 - - + -
3688J GLY* 3.4 39.3 - - - +
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Residues in contact with MET3527 (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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2845H VAL* 6.6 0.4 - - + -
3523J LEU* 2.8 32.8 + - + +
3524J GLU* 5.0 2.2 - - - +
3526J VAL* 1.3 72.1 - - + +
3528J PRO* 1.3 68.3 - - + +
3529J SER 2.9 1.4 + - - -
3530J VAL* 2.9 31.2 + - + +
3595J SER* 3.6 23.3 - - - +
3644J ILE* 4.0 31.4 - - + -
3652J GLU* 4.0 32.5 - - + +
3654J VAL* 5.2 9.9 - - + -
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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