Contacts of the strand formed by residues 3557 - 3571 (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 GLN3557 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3540J THR* 4.7 1.8 + - - +
3541J VAL* 3.1 38.8 + - + +
3542J ASN 3.8 2.1 - - - +
3543J THR* 3.7 14.5 - - - +
3544J PRO* 3.4 28.6 - - - +
3556J GLY* 1.3 77.4 - - - +
3558J GLN* 1.3 69.1 + - - +
3559J GLN* 3.2 26.7 + - - +
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Residues in contact with GLN3558 (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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3538J SER* 3.4 26.9 + - - +
3539J THR* 3.0 18.2 - - - +
3540J THR* 2.4 30.0 + - - +
3557J GLN* 1.3 75.6 + - - +
3559J GLN* 1.3 73.7 - - - +
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Residues in contact with GLN3559 (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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3538J SER* 3.0 6.5 - - - -
3539J THR* 2.7 41.1 + - + +
3541J VAL* 3.0 37.5 - - + +
3557J GLN* 3.2 27.9 + - - +
3558J GLN* 1.3 94.3 - - - +
3560J LYS* 1.3 69.5 + - - +
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Residues in contact with LYS3560 (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* 5.2 17.0 + - + +
3537J GLY 3.3 11.0 - - - +
3538J SER* 4.1 7.6 - - - -
3559J GLN* 1.3 82.1 + - - +
3561J PHE* 1.3 61.7 + - - +
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Residues in contact with PHE3561 (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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3535J VAL* 4.5 6.7 - - + -
3536J GLU* 3.7 4.1 - - - +
3537J GLY* 2.8 61.0 + - - +
3538J SER* 3.3 22.0 - - - -
3539J THR* 4.0 13.9 - - + -
3559J GLN 4.8 0.4 - - - +
3560J LYS* 1.3 77.2 - - - +
3562J MET* 1.3 79.8 + - - +
3563J ALA* 4.2 19.3 - - + -
3583J VAL 5.1 0.7 - - - -
3585J ASP 3.9 16.2 - - - -
3586J ASN* 3.7 18.6 - - + -
3587J ALA 4.7 0.2 - - - -
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Residues in contact with MET3562 (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* 6.0 5.2 - - - +
3535J VAL 3.4 9.4 - - - +
3536J GLU* 5.1 9.0 - - + +
3561J PHE* 1.3 86.2 - - - +
3563J ALA* 1.3 63.1 + - - +
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Residues in contact with ALA3563 (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* 3.6 4.0 + - - +
3535J VAL* 2.8 36.2 + - + +
3561J PHE* 4.2 12.3 - - + -
3562J MET* 1.3 75.9 - - - +
3564J LEU* 1.3 66.1 + - - +
3582J HIS 5.2 2.5 - - - +
3583J VAL* 3.6 30.1 - - + +
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Residues in contact with LEU3564 (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 3.1 11.2 - - - +
3534J ASN* 4.1 17.0 - - - +
3563J ALA* 1.3 80.2 - - - +
3565J GLY* 1.3 59.7 + - - +
3583J VAL* 3.8 10.1 - - - +
3646J ASN* 3.8 36.1 - - - +
3648J PHE 5.3 0.2 - - - -
3649J GLY* 3.8 26.2 - - - +
3678J ASN* 5.5 11.8 + - - +
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Residues in contact with GLY3565 (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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3532J SER* 3.7 3.3 - - - -
3533J ILE* 2.9 32.9 + - - +
3564J LEU* 1.3 78.7 - - - +
3566J SER* 1.3 64.1 + - - -
3583J VAL* 3.7 20.0 - - - +
3646J ASN* 4.8 9.8 - - - +
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Residues in contact with SER3566 (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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3530J VAL* 4.6 5.6 - - - -
3531J VAL 3.5 9.2 - - - -
3532J SER* 4.7 0.2 - - - +
3533J ILE* 4.0 4.0 - - - -
3565J GLY* 1.3 74.1 - - - -
3567J GLY* 1.3 55.2 + - - +
3579J THR* 2.6 29.7 + - - -
3580J ASN* 4.4 7.4 + - - +
3644J ILE 4.6 1.3 - - - -
3645J GLY* 3.5 13.2 - - - -
3646J ASN 3.4 20.7 + - - +
3652J GLU* 3.2 21.5 + - - -
3680J GLY* 4.9 4.8 + - - -
3681J GLY* 4.5 16.6 - - - -
3682J ALA 5.4 0.7 - - - -
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Residues in contact with GLY3567 (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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3530J VAL* 3.6 5.7 - - - +
3531J VAL* 3.0 29.8 + - - +
3533J ILE* 4.0 4.1 - - - +
3566J SER* 1.3 76.0 - - - +
3568J VAL* 1.3 68.0 + - - +
3577J VAL* 3.7 14.1 - - - -
3578J VAL 3.0 14.4 - - - -
3579J THR* 3.9 2.5 - - - -
3681J GLY* 6.1 1.3 - - - -
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Residues in contact with VAL3568 (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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3529J SER* 3.6 7.4 - - - +
3530J VAL* 4.5 8.1 - - + -
3567J GLY* 1.3 79.9 - - - +
3569J ILE* 1.3 66.9 + - - +
3570J ILE* 3.3 7.2 + - + -
3577J VAL* 3.2 4.4 - - - +
3578J VAL* 2.8 50.1 + - + +
3627J ILE* 3.3 41.3 - - + -
3681J GLY 5.4 0.2 - - - -
3682J ALA* 3.5 36.1 - - + +
3690J LEU* 4.5 7.4 - - + -
3693J ILE* 4.9 3.1 - - + -
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Residues in contact with ILE3569 (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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3528J PRO 3.9 11.2 - - - +
3529J SER* 2.9 14.9 + - - +
3531J VAL* 3.6 15.0 - - + -
3568J VAL* 1.3 70.2 - - - +
3570J ILE* 1.3 65.8 + - - +
3571J ASP 4.3 6.5 - - - +
3572J ALA* 4.3 11.4 - - - -
3576J TYR 3.5 7.0 - - - +
3577J VAL* 3.9 10.5 - - + -
3594J LEU* 3.7 29.4 - - + -
3618J ILE* 4.6 2.7 - - + -
3624J LEU* 3.8 19.1 - - + -
3625J THR 3.0 34.5 - - - +
3626J ALA* 3.6 10.1 - - + -
3627J ILE 3.1 25.6 + - - -
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Residues in contact with ILE3570 (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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3568J VAL* 3.6 16.4 - - + +
3569J ILE* 1.3 74.8 - - - +
3571J ASP* 1.3 59.0 + - + +
3576J TYR* 2.6 27.5 + - + +
3578J VAL* 4.3 12.3 - - + -
3615J LEU* 5.1 7.6 - - + -
3626J ALA* 4.0 10.2 - - - +
3627J ILE* 3.4 35.2 - - + +
3629J MET* 3.1 39.8 - - + +
3690J LEU* 3.9 12.1 - - + -
3716J VAL* 6.0 1.3 - - + -
3720J THR* 4.8 17.5 - - + +
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Residues in contact with ASP3571 (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* 3.7 3.3 - - - +
3570J ILE* 1.3 80.0 - - + +
3572J ALA* 1.3 58.8 + - - +
3573J ASP* 3.0 20.1 + - - +
3574J LYS* 3.0 32.4 + - - +
3575J GLY* 2.8 27.5 + - - -
3576J TYR* 3.1 35.2 + - + +
3626J ALA* 4.4 0.4 - - - -
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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