Contacts of the helix formed by residues 521 - 533 (chain A) in PDB entry 2EZT
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 GLN 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515A ARG 5.3 1.6 + - - -
516A VAL* 3.4 20.1 - - + -
517A ASN* 2.9 33.0 + - - +
518A LYS* 3.1 46.2 + - + +
520A GLU* 1.3 80.7 - - + +
522A LEU* 1.3 64.3 + - - +
523A PRO* 3.6 1.0 - - - -
524A ASP* 3.8 4.9 + - - +
525A VAL* 3.4 24.1 + - + +
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Residues in contact with LEU 522 (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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371A LEU* 3.4 35.9 - - + -
375A GLN* 3.5 33.9 - - + +
376A VAL* 4.5 6.1 - - + -
378A ARG* 4.2 8.1 - - - +
379A ALA* 4.1 11.4 - - + -
516A VAL* 3.9 20.6 - - + -
518A LYS 4.2 1.6 - - - +
519A ILE* 3.4 12.6 - - - +
521A GLN* 1.3 75.9 - - - +
523A PRO* 1.4 75.8 - - + +
524A ASP 3.2 0.2 + - - -
525A VAL* 3.2 2.4 + - - -
526A PHE* 2.9 50.3 + - + +
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Residues in contact with PRO 523 (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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367A GLN* 5.7 4.7 - - - +
378A ARG* 4.5 13.5 - - - +
379A ALA* 5.9 1.1 - - + -
519A ILE 3.9 5.6 - - - +
520A GLU* 3.7 13.5 - - - +
521A GLN 3.7 3.8 - - - -
522A LEU* 1.4 95.8 - - + +
524A ASP* 1.3 61.4 + - - +
526A PHE* 4.0 2.8 - - + +
527A GLU* 3.1 30.2 + - + +
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Residues in contact with ASP 524 (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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520A GLU 5.5 0.2 + - - -
521A GLN* 3.8 5.1 + - - +
522A LEU 3.3 0.6 - - - -
523A PRO* 1.3 78.9 - - - +
525A VAL* 1.3 69.4 + - + +
527A GLU* 3.6 7.1 + - - +
528A GLN* 3.2 42.0 + - - +
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Residues in contact with VAL 525 (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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514A PHE* 3.7 41.2 - - + -
516A VAL* 3.6 28.3 - - + -
521A GLN* 3.4 14.6 + - + +
522A LEU 3.2 3.6 + - - +
524A ASP* 1.3 82.1 - - + +
526A PHE* 1.3 61.3 + - + +
528A GLN* 3.3 9.2 + - - +
529A ALA* 2.9 26.3 + - - +
540A ILE* 3.8 23.3 - - + -
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Residues in contact with PHE 526 (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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376A VAL* 3.9 23.1 - - + -
379A ALA* 3.7 26.5 - - + +
380A VAL* 3.9 23.8 - - + -
383A ILE* 3.5 38.6 - - + +
468A ILE* 5.5 0.4 - - + -
470A VAL* 4.3 10.1 - - + -
522A LEU* 2.9 48.4 + - + +
523A PRO* 4.0 2.7 - - + +
525A VAL* 1.3 79.3 - - + +
527A GLU* 1.3 58.3 + - - +
529A ALA* 3.7 3.5 - - - +
530A LYS* 2.9 29.6 + - - +
540A ILE* 3.7 35.7 - - + -
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Residues in contact with GLU 527 (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 LYS* 4.9 6.6 - - - +
383A ILE* 3.7 17.2 - - - +
523A PRO* 3.1 24.3 + - + +
524A ASP* 3.9 9.2 - - - +
526A PHE* 1.3 73.8 - - - +
528A GLN* 1.3 65.6 + - + +
530A LYS* 3.4 19.1 + - - +
531A ALA* 3.2 22.2 + - - +
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Residues in contact with GLN 528 (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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512A GLN* 6.0 0.8 - - - +
514A PHE* 3.6 35.4 - - + -
524A ASP* 3.2 36.9 + - - +
525A VAL* 3.3 10.7 + - - +
527A GLU* 1.3 77.9 - - + +
529A ALA* 1.3 55.6 + - - +
531A ALA* 3.2 7.7 + - - +
532A ILE* 2.9 37.9 + - + +
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Residues in contact with ALA 529 (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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383A ILE* 5.0 1.1 - - + -
468A ILE* 4.7 8.1 - - + -
514A PHE* 4.4 1.3 - - + -
525A VAL 2.9 10.8 + - - +
526A PHE 3.7 4.7 - - - +
527A GLU 3.3 0.2 - - - -
528A GLN* 1.3 74.8 - - - +
530A LYS* 1.3 56.1 + - - +
532A ILE* 3.4 2.4 + - - +
533A ALA* 2.9 34.6 + - - +
538A VAL* 3.8 31.7 - - + +
540A ILE* 3.6 32.1 - - + -
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Residues in contact with LYS 530 (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 LYS 5.6 0.2 - - - -
383A ILE* 2.8 52.4 + - + +
384A ALA 4.9 0.2 - - - -
385A GLU* 2.8 29.6 + - - +
440A GLN* 4.0 8.1 + - - +
468A ILE* 4.4 10.6 - - - +
526A PHE 2.9 17.7 + - - +
527A GLU* 3.5 18.8 - - - +
529A ALA* 1.3 76.2 - - - +
531A ALA* 1.3 60.4 + - - +
533A ALA* 3.7 3.6 + - - +
534A GLN* 3.1 36.6 + - - +
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Residues in contact with ALA 531 (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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527A GLU 3.2 8.0 + - - +
528A GLN* 3.2 10.4 + - - +
530A LYS* 1.3 76.2 - - - +
532A ILE* 1.3 65.8 + - - +
533A ALA 3.2 1.1 - - - -
534A GLN* 3.0 27.6 + - - +
535A HIS* 4.4 2.1 + - - -
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Residues in contact with ILE 532 (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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512A GLN* 3.8 38.6 - - + +
514A PHE* 3.7 35.4 - - + -
528A GLN* 2.9 27.4 + - + +
529A ALA 3.7 3.1 - - - +
531A ALA* 1.3 70.4 - - + +
533A ALA* 1.3 57.6 + - - +
535A HIS* 2.9 21.1 + - - +
536A GLU* 3.0 18.5 + - + +
537A PRO 3.7 23.6 - - - +
538A VAL* 3.8 15.9 - - + -
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Residues in contact with ALA 533 (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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433A LYS* 5.1 2.9 + - - -
440A GLN* 6.2 0.7 - - + -
466A PRO* 3.3 26.3 - - - +
468A ILE* 3.5 31.6 - - + -
529A ALA 2.9 16.6 + - - +
530A LYS 4.0 5.4 - - - +
531A ALA 3.2 0.4 - - - -
532A ILE* 1.3 72.4 - - - +
534A GLN* 1.3 65.2 + - - +
535A HIS 3.1 0.7 - - - -
536A GLU 3.2 14.1 - - - +
538A VAL* 4.2 4.0 - - + -
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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