Contacts of the helix formed by residues 573 - 584 (chain A) in PDB entry 5I75
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 TRP 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A LEU* 4.1 31.4 - - + -
246A GLN* 4.3 15.5 - - + +
571A PRO* 3.2 29.3 - - + +
572A TYR* 1.3 102.8 - + + +
574A SER* 1.3 67.5 + - - +
575A ILE 3.2 3.1 - - - -
576A ILE* 2.9 35.8 + - + +
577A LEU* 3.2 29.5 + - + -
703A CLR 3.2 76.5 - - + -
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Residues in contact with SER 574 (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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245A LEU* 4.1 5.2 - - - +
491A LEU* 3.6 24.3 - - - +
495A TYR* 3.7 12.8 - - - -
570A TYR* 3.6 14.8 - - - +
571A PRO* 2.9 37.6 + - - +
572A TYR 3.3 0.2 - - - -
573A TRP* 1.3 85.2 - - - +
575A ILE* 1.3 58.0 + - - +
577A LEU* 3.0 5.3 + - - +
578A GLY 2.9 25.3 + - - -
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Residues in contact with ILE 575 (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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495A TYR* 3.6 39.0 - - + +
556A PHE* 4.6 0.9 - - + -
560A PRO* 4.0 21.8 - - + -
572A TYR 3.7 17.2 + - - +
574A SER* 1.3 78.4 - - - +
576A ILE* 1.3 67.3 + - + +
579A TYR* 3.0 68.8 + - + +
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Residues in contact with ILE 576 (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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572A TYR* 4.9 6.7 - - + +
573A TRP* 2.9 32.9 + - + +
575A ILE* 1.3 87.8 - - + +
577A LEU* 1.3 56.5 + - - +
579A TYR* 3.9 4.9 - - - +
580A ALA* 3.0 28.1 + - + +
703A CLR 4.9 25.1 - - + -
704A C14 4.4 17.7 - - + +
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Residues in contact with LEU 577 (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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245A LEU* 5.3 2.2 - - + -
491A LEU* 3.7 26.2 - - + -
573A TRP* 3.2 29.1 + - + +
574A SER 3.0 7.7 + - - +
576A ILE* 1.3 76.7 - - - +
578A GLY* 1.3 60.0 + - - +
580A ALA* 3.0 8.4 + - + +
581A ILE* 2.8 50.7 + - + +
703A CLR 3.6 41.0 - - + +
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Residues in contact with GLY 578 (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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491A LEU* 4.5 6.2 - - - +
495A TYR* 3.4 36.2 - - - +
496A ALA* 3.8 8.2 - - - -
574A SER 2.9 11.3 + - - -
575A ILE 4.0 0.2 - - - -
577A LEU* 1.3 76.7 - - - +
579A TYR* 1.3 50.6 + - - +
581A ILE* 3.0 6.4 + - - +
582A GLY* 2.6 34.3 + - - -
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Residues in contact with TYR 579 (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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495A TYR 4.1 8.3 - - - -
499A PRO* 4.8 4.5 - - + -
556A PHE* 3.8 19.3 - + - -
557A LEU* 3.2 30.3 + - + +
560A PRO* 3.8 19.3 - - + +
575A ILE* 3.0 46.0 + - + +
576A ILE* 4.0 4.0 - - - +
578A GLY* 1.3 73.6 - - - +
580A ALA* 1.3 55.3 + - - +
582A GLY* 4.1 2.5 - - - +
583A THR* 2.7 40.0 + - - +
704A C14 3.6 56.5 - - + -
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Residues in contact with ALA 580 (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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576A ILE 3.0 16.4 + - - +
577A LEU* 3.0 12.4 + - + +
579A TYR* 1.3 78.6 - - - +
581A ILE* 1.3 61.6 + - - +
583A THR* 3.3 5.9 + - - -
584A SER* 3.1 26.0 + - - -
703A CLR 3.6 42.4 - - + +
704A C14 4.0 13.4 - - + +
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Residues in contact with ILE 581 (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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171A TYR* 3.5 43.2 - - + +
491A LEU* 5.3 1.1 - - + -
492A LEU* 3.9 28.9 - - + -
496A ALA* 4.0 14.8 - - + -
577A LEU* 2.8 41.4 + - + +
578A GLY* 3.6 7.0 - - - +
580A ALA* 1.3 76.6 - - + +
582A GLY* 1.3 63.8 + - - +
584A SER* 2.8 19.7 + - - -
585A SER 3.4 4.9 + - - -
703A CLR 5.2 9.0 - - + -
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Residues in contact with GLY 582 (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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171A TYR* 6.0 0.4 - - - -
495A TYR 5.3 0.4 - - - -
496A ALA* 4.0 20.4 - - - +
499A PRO* 5.9 1.8 - - - -
500A ALA* 4.2 3.5 - - - +
578A GLY 2.6 18.6 + - - -
579A TYR* 3.0 4.9 + - - -
581A ILE* 1.3 73.6 - - - +
583A THR* 1.3 59.3 + - - +
585A SER* 2.3 32.0 + - - -
586A PHE* 3.1 12.3 - - - -
704A C14 5.3 2.7 - - - -
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Residues in contact with THR 583 (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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579A TYR 2.7 25.4 + - - +
580A ALA* 3.3 8.8 + - - -
582A GLY* 1.3 71.2 - - - -
584A SER* 1.3 59.6 + - - +
585A SER 2.9 6.1 + - - -
586A PHE* 3.0 29.9 + - + -
587A ILE* 3.2 18.5 + - - +
704A C14 3.7 54.0 - - + +
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Residues in contact with SER 584 (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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167A ILE* 4.3 8.7 - - - +
171A TYR* 3.3 16.3 + - - -
580A ALA 3.1 14.0 + - - -
581A ILE* 2.8 23.4 + - - -
583A THR* 1.3 80.0 + - - +
585A SER* 1.3 60.9 + - - +
587A ILE* 3.4 32.6 - - - +
703A CLR 5.2 14.2 - - - +
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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