Contacts of the helix formed by residues 517 - 529 (chain A) in PDB entry 5I74
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 GLY 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A VAL 3.3 13.5 + - - +
513A SER 3.3 12.5 + - - -
514A TRP 5.0 1.1 - - - -
515A PHE 3.0 6.8 - - - -
516A TYR* 1.3 92.4 - - - +
518A ILE* 1.3 64.2 - - - -
519A THR* 3.4 5.8 - - - -
520A GLN 4.3 2.5 - - - -
521A PHE* 3.6 7.3 + - - +
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Residues in contact with ILE 518 (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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135A MET* 5.8 1.3 - - + -
512A VAL* 5.6 2.5 - - + +
513A SER* 3.3 21.2 + - - +
517A GLY* 1.3 73.4 - - - -
519A THR* 1.3 73.4 + - + +
520A GLN 3.4 0.2 - - - -
521A PHE* 3.2 16.8 + - + +
522A CYS* 2.9 33.8 + - - -
538A ARG* 4.4 3.8 - - + +
541A TRP* 3.5 46.4 - - + -
542A VAL* 3.5 34.3 - - + -
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Residues in contact with THR 519 (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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517A GLY* 4.9 2.6 - - - -
518A ILE* 1.3 89.6 + - + +
520A GLN* 1.3 64.3 + - - +
522A CYS* 3.2 9.3 + - - +
523A ARG* 2.9 27.6 + - - +
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Residues in contact with GLN 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 5.4 0.2 + - - -
516A TYR* 3.2 42.5 + - + +
517A GLY* 4.1 1.4 + - - -
518A ILE 3.4 0.2 - - - -
519A THR* 1.3 83.0 + - - +
521A PHE* 1.3 58.4 + - - +
523A ARG* 3.2 28.9 + - - +
524A ASP* 2.9 51.5 + - - +
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Residues in contact with PHE 521 (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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134A TYR* 4.9 1.1 - + - -
135A MET* 3.7 27.4 - - + -
138A ALA* 4.0 15.3 - - + -
139A LEU* 3.6 38.1 - - + -
512A VAL* 4.6 8.7 - - + -
516A TYR* 3.8 8.1 - + + -
517A GLY 3.6 14.4 + - - +
518A ILE* 3.2 28.7 + - + +
519A THR 3.2 0.4 - - - -
520A GLN* 1.3 77.7 - - - +
522A CYS* 1.3 56.7 + - - +
524A ASP* 3.1 12.7 + - + +
525A VAL* 2.9 48.8 + - + +
541A TRP* 3.6 37.2 - + - -
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Residues in contact with CYS 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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518A ILE* 2.9 28.1 + - - -
519A THR* 3.2 9.8 + - - +
521A PHE* 1.3 75.5 - - - +
523A ARG* 1.3 58.1 + - - +
526A LYS* 2.9 27.2 + - - +
532A SER* 3.7 12.4 + - - +
533A PRO* 3.4 37.5 - - + +
538A ARG* 4.3 12.8 - - - -
541A TRP* 3.9 16.8 - - - -
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Residues in contact with ARG 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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142A TYR* 5.0 5.1 + - - -
519A THR 2.9 14.5 + - - +
520A GLN* 3.4 35.5 - - - +
521A PHE 3.1 0.2 - - - -
522A CYS* 1.3 75.9 - - - +
524A ASP* 1.3 62.8 + - - +
526A LYS* 3.1 32.5 + - - +
527A GLU* 2.9 43.4 + - - +
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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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139A LEU* 5.7 1.3 - - + +
142A TYR* 3.0 48.5 + - + -
143A HIS* 5.0 1.4 - - - -
516A TYR* 2.3 33.2 + - - -
520A GLN* 2.9 33.5 + - - +
521A PHE* 3.1 10.7 + - + +
523A ARG* 1.3 77.8 + - - +
525A VAL* 1.3 61.1 + - + +
527A GLU* 2.9 7.6 + - - +
528A MET* 2.9 31.5 + - - +
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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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134A TYR* 3.2 27.6 - - + +
138A ALA* 4.6 10.1 - - + -
521A PHE* 2.9 43.0 + - + +
524A ASP* 1.3 76.3 - - + +
526A LYS* 1.3 57.4 + - - +
528A MET* 4.5 6.5 - - - +
529A LEU* 2.9 45.9 + - + +
531A PHE* 3.4 5.7 - - + +
533A PRO* 3.7 28.5 - - + -
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Residues in contact with LYS 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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522A CYS 2.9 15.6 + - - +
523A ARG* 3.1 37.3 + - - +
525A VAL* 1.3 77.8 - - - +
527A GLU* 1.3 55.7 - - - +
530A GLY* 3.1 27.2 + - - +
531A PHE* 3.4 14.3 + - - -
532A SER* 3.6 26.0 - - - +
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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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142A TYR* 4.8 5.8 - - + +
353A PHE* 4.2 25.4 - - + -
354A ASN* 5.3 3.3 + - - +
523A ARG* 2.9 32.3 + - - +
524A ASP* 2.9 11.4 + - - +
526A LYS* 1.3 78.3 - - - +
528A MET* 1.3 65.8 + - - +
530A GLY* 3.9 3.8 + - - -
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Residues in contact with MET 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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138A ALA* 4.3 6.1 - - - +
141A GLN* 3.4 45.1 - - + +
142A TYR* 3.6 44.0 - - + -
353A PHE* 3.3 39.5 - - + +
354A ASN* 3.8 31.4 + - - +
355A ASN 4.3 1.8 - - - +
357A CYS* 3.8 10.5 - - - -
524A ASP 2.9 17.4 + - - +
525A VAL* 4.2 2.9 - - - +
527A GLU* 1.3 80.2 - - - +
529A LEU* 1.3 69.3 + - + +
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Residues in contact with LEU 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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134A TYR* 3.9 18.2 - - - +
354A ASN* 5.6 2.0 - - - -
355A ASN 4.6 3.1 - - - +
356A ASN* 4.1 23.1 - - - +
357A CYS* 4.2 26.0 - - - +
358A TYR* 4.1 13.7 - - + +
525A VAL* 2.9 31.8 + - + +
528A MET* 1.3 86.7 - - + +
530A GLY* 1.3 56.0 + - - +
531A PHE* 3.2 52.3 - - + +
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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