Contacts of the helix formed by residues 525 - 533 (chain A) in PDB entry 5H65
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 ILE 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A LEU* 5.6 1.0 - - - +
523A SER* 4.1 27.1 - - - +
524A TRP* 1.3 71.4 - - - +
526A PRO* 1.4 77.9 - - + +
527A SER* 3.5 21.8 - - - +
528A SER* 3.0 23.9 + - - +
529A VAL* 2.9 20.1 + - - +
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Residues in contact with PRO 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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492A PHE* 3.9 6.6 - - + -
493A LEU* 3.9 16.8 - - + -
495A GLN* 3.3 22.2 - - - +
500A HIS* 3.4 38.4 - - + +
524A TRP 3.5 6.5 - - - +
525A ILE* 1.4 88.9 - - + +
527A SER* 1.3 56.6 + - - +
529A VAL* 3.2 4.6 + - + +
530A ALA* 2.9 29.0 + - - +
537A PRO* 5.7 0.9 - - - -
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Residues in contact with SER 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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525A ILE* 3.5 14.9 - - - +
526A PRO* 1.3 78.0 - - - +
528A SER* 1.3 60.3 + - - +
530A ALA* 3.5 7.7 + - - +
531A GLU* 3.0 30.0 + - - +
537A PRO* 4.7 12.1 - - - +
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Residues in contact with SER 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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518A LEU* 3.5 26.9 - - - +
525A ILE* 3.0 27.9 + - - +
527A SER* 1.3 79.3 + - - +
529A VAL* 1.3 65.1 + - - +
531A GLU* 3.5 9.9 + - - +
532A ALA* 3.1 18.9 + - - +
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Residues in contact with VAL 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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474A ILE* 4.1 18.2 - - + -
492A PHE* 4.1 13.5 - - + -
493A LEU* 4.4 17.9 - - + -
515A LEU* 4.4 3.8 - - + -
518A LEU* 4.2 8.3 - - + -
524A TRP* 4.0 33.9 - - + -
525A ILE 2.9 20.3 + - - +
526A PRO* 3.5 8.3 - - + +
528A SER* 1.3 73.7 - - - +
530A ALA* 1.3 63.4 + - - +
532A ALA* 3.4 5.4 + - - +
533A LEU* 3.2 40.1 + - + +
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Residues in contact with ALA 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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492A PHE* 3.7 24.7 - - + -
526A PRO 2.9 16.3 + - - +
527A SER 3.6 5.6 - - - +
528A SER 3.3 0.2 - - - -
529A VAL* 1.3 76.3 - - - +
531A GLU* 1.3 59.3 - - - +
533A LEU 3.2 2.3 + - - -
534A GLY 3.0 4.2 + - - -
535A ILE* 2.7 51.7 + - + +
537A PRO* 3.8 17.0 - - + -
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Residues in contact with GLU 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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510A ARG* 3.3 14.4 + - - +
527A SER 3.0 17.6 + - - +
528A SER* 3.8 8.7 - - - +
529A VAL 3.4 0.2 - - - -
530A ALA* 1.3 74.8 - - - +
532A ALA* 1.3 63.3 + - - +
534A GLY* 3.1 12.8 + - - +
535A ILE 4.1 4.2 + - - +
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Residues in contact with ALA 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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510A ARG* 3.0 31.8 + - - +
514A ASN* 3.3 28.6 - - - +
515A LEU* 4.2 5.6 - - + -
517A SER* 3.9 8.7 - - - +
518A LEU* 4.2 19.5 - - + -
528A SER 3.1 13.7 + - - +
529A VAL 3.6 9.0 - - - +
530A ALA 3.3 0.2 - - - -
531A GLU* 1.3 75.7 - - - +
533A LEU* 1.3 57.6 + - - +
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Residues in contact with LEU 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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474A ILE* 4.4 11.9 - - + -
485A LEU* 4.9 12.6 - - + -
492A PHE* 4.8 3.1 - - + -
509A LEU* 3.5 8.4 - - + +
510A ARG* 2.8 48.0 + - - +
511A SER 3.9 11.9 - - - +
512A ILE* 4.2 15.0 - - + +
515A LEU* 4.1 25.1 - - + +
529A VAL* 3.2 30.7 + - + +
530A ALA 3.2 2.0 + - - +
531A GLU 3.2 0.8 - - - -
532A ALA* 1.3 77.7 - - - +
534A GLY* 1.3 60.7 + - - +
535A ILE* 3.3 26.0 - - + -
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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