Contacts of the strand formed by residues 428 - 434 (chain A) in PDB entry 4EZJ
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 LEU 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ASN 3.3 2.9 - - - +
387A ILE* 3.4 4.7 - - - -
388A GLN* 2.9 52.3 + - + +
389A HIS* 6.3 0.9 - - - -
426A GLY 4.3 4.7 - - - +
427A ALA* 1.3 75.2 - - - +
429A LEU* 1.3 62.5 + - - +
430A ASN* 3.7 1.1 + - + +
465A ASN* 3.7 31.9 - - + +
466A LEU 3.5 17.7 - - - +
467A LEU* 3.9 22.0 - - + +
468A LEU* 4.0 7.8 - - - +
502A LEU* 3.8 30.7 - - + +
504A SER* 4.9 4.7 - - - -
636A SER* 6.1 1.3 - - - +
671A PRO* 6.5 1.1 - - + -
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A PHE* 4.6 10.1 - - + -
363A VAL* 3.9 31.9 - - + -
385A ALA* 4.1 14.1 - - + -
386A ASN 3.5 12.3 - - - +
387A ILE* 4.9 2.2 - - + -
416A PHE* 4.8 2.5 - - + -
428A LEU* 1.3 72.6 - - - +
430A ASN* 1.3 58.4 + - - +
431A LEU* 3.8 35.2 + - + +
464A VAL 4.0 0.5 - - - +
465A ASN* 3.3 4.0 - - - +
466A LEU* 2.7 54.1 + - + +
468A LEU* 3.7 22.3 - - + +
518A ILE* 4.7 2.0 - - + -
520A LEU* 4.4 11.7 - - + -
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Residues in contact with ASN 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A GLU 3.2 3.1 - - - +
385A ALA* 3.6 0.2 - - - -
386A ASN* 2.8 64.8 + - + +
388A GLN* 3.2 32.3 + - + +
428A LEU* 3.7 2.4 + - + +
429A LEU* 1.3 70.8 - - - +
431A LEU* 1.3 61.1 + - - +
432A GLN* 3.1 31.6 + - - +
463A TYR* 4.5 5.7 - - - +
464A VAL 4.0 3.0 + - - -
465A ASN* 2.8 27.9 + - - +
501A LYS* 4.4 8.1 + - - +
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Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 5.1 0.4 - - + -
365A ILE* 3.8 26.5 - - + -
383A VAL* 4.9 2.2 - - + -
384A GLU 3.4 2.9 - - - +
385A ALA* 3.9 10.3 - - + -
429A LEU* 3.8 42.6 - - + +
430A ASN* 1.3 71.2 - - - +
432A GLN* 1.3 63.7 + - - +
463A TYR* 3.4 3.3 - - - -
464A VAL* 3.0 45.8 + - + +
466A LEU* 5.5 1.8 - - + -
482A LEU* 4.4 12.6 - - + -
484A MET* 3.8 5.2 - - + +
516A ILE* 4.3 25.6 - - + -
518A ILE* 4.2 20.2 - - + -
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Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A PHE 3.6 0.2 - - - +
383A VAL* 3.3 7.8 - - - +
384A GLU* 2.8 42.6 + - + +
386A ASN* 4.2 5.2 - - - +
388A GLN* 5.4 1.2 + - - +
430A ASN* 3.1 34.1 + - - +
431A LEU* 1.3 76.6 - - - +
433A ILE* 1.4 63.7 + - - +
434A TYR* 3.0 35.3 + - + -
460A LEU* 3.5 22.4 - - + +
462A TYR 3.5 5.4 - - - +
463A TYR* 3.7 3.9 - - + +
484A MET* 4.8 0.4 - - - -
501A LYS* 2.9 33.5 + - - +
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ILE* 3.7 28.5 - - + -
381A VAL* 3.8 28.9 - - + -
382A PHE 3.3 6.1 - - - +
383A VAL* 4.1 16.4 - - + -
432A GLN* 1.4 77.3 - - - +
434A TYR* 1.4 59.8 + - - +
460A LEU* 3.4 5.7 - - - +
461A LEU* 2.8 32.7 + - + -
462A TYR* 3.0 29.5 + - + +
484A MET* 3.7 28.0 - - + -
514A MET* 3.8 19.1 - - + -
516A ILE* 5.5 0.9 - - + -
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Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A THR 4.1 0.3 - - - -
381A VAL* 3.3 29.1 - - - +
382A PHE* 3.2 52.7 + + + -
384A GLU* 2.6 49.0 + - + -
432A GLN* 3.0 22.4 + - + -
433A ILE* 1.4 75.1 - - - +
435A CYS* 1.3 62.3 + - - +
460A LEU* 3.3 43.5 - - + +
461A LEU* 4.6 1.3 - - - +
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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