Contacts of the helix formed by residues 522 - 531 (chain A) in PDB entry 3TXO
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 ALA 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A TYR 3.4 5.8 + - - +
521A ILE* 1.3 78.6 - - - +
523A PRO* 1.3 73.9 - - + +
524A GLU* 3.3 25.1 - - - +
525A ILE* 3.1 23.6 + - + +
526A LEU* 3.2 9.8 + - - +
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Residues in contact with PRO 523 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A ILE 3.9 2.7 - - - +
522A ALA* 1.3 87.7 - - + +
524A GLU* 1.4 63.6 + - - +
526A LEU* 3.4 12.4 + - + +
527A GLN* 3.0 34.9 + - + +
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Residues in contact with GLU 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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522A ALA* 3.5 25.7 - - - +
523A PRO* 1.4 80.6 - - - +
525A ILE* 1.3 71.5 + - + +
527A GLN* 3.8 17.3 + - - +
528A GLU* 3.5 19.8 + - - +
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Residues in contact with ILE 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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521A ILE* 3.7 17.3 - - + -
522A ALA* 3.1 24.3 + - + +
524A GLU* 1.3 88.0 - - + +
526A LEU* 1.3 64.7 + - - +
528A GLU* 3.3 9.2 + - + +
529A MET* 3.0 35.6 + - + +
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Residues in contact with LEU 526 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A PRO 6.0 0.7 - - - +
521A ILE* 3.8 38.6 - - + +
522A ALA 3.2 7.2 + - - +
523A PRO* 3.4 12.5 + - + +
525A ILE* 1.3 76.0 - - - +
527A GLN* 1.3 55.0 + - - +
529A MET* 3.1 21.1 + - + -
530A LEU* 2.7 58.4 + - + +
531A TYR* 5.0 0.9 - - - -
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Residues in contact with GLN 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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523A PRO* 3.0 22.4 + - + +
524A GLU* 3.8 17.0 + - - +
526A LEU* 1.3 73.1 - - - +
528A GLU* 1.3 58.2 + - - +
531A TYR* 2.8 43.5 + - + +
592A ASN* 3.5 20.1 - - - +
593A PRO* 3.7 31.5 - - + +
594A THR* 4.6 12.9 - - + +
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Residues in contact with GLU 528 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A LYS* 3.3 26.0 + - - -
524A GLU 3.5 10.1 + - - +
525A ILE* 3.3 13.7 + - + +
526A LEU 3.3 0.6 - - - -
527A GLN* 1.3 77.3 - - - +
529A MET* 1.3 83.1 + - - +
531A TYR 5.0 0.4 - - - -
532A GLY* 3.4 23.5 + - - +
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Residues in contact with MET 529 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505A ILE* 5.6 5.0 - - - +
506A CYS 5.1 3.5 - - - +
521A ILE* 4.8 13.5 - - + -
525A ILE* 3.0 35.7 + - + +
526A LEU* 3.6 24.5 - - + +
528A GLU* 1.3 89.3 + - - +
530A LEU* 1.3 75.2 + - + +
532A GLY 4.6 1.6 + - - -
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Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A CYS 4.1 19.4 - - - +
526A LEU* 2.7 44.4 + - + +
529A MET* 1.3 92.9 - - + +
531A TYR* 1.3 79.5 + - + +
532A GLY 3.6 1.5 + - - -
533A PRO* 4.8 0.7 - - - +
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Residues in contact with TYR 531 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A GLN* 2.8 32.3 + - + +
528A GLU* 4.7 0.7 - - - -
530A LEU* 1.3 101.5 - - + +
532A GLY* 1.3 64.6 + - - +
533A PRO* 3.4 6.5 - - - -
534A ALA* 3.2 23.9 + - + +
535A VAL* 4.4 2.4 + - - +
593A PRO* 4.2 13.0 - - + +
594A THR* 3.7 40.3 - - + +
599A SER* 4.1 24.2 - - - -
600A LEU* 5.2 13.2 - - + -
601A THR* 6.1 1.6 - - - +
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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