Contacts of the helix formed by residues 521 - 527 (chain S) in PDB entry 1I84
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 LEU 521 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487S GLU* 3.5 42.8 - - + +
490S GLN* 3.6 23.3 - - + -
491S GLN* 2.6 24.2 + - + +
494S ASN* 4.0 10.1 - - - +
519S LEU* 4.5 6.1 - - + -
520S ASP* 1.3 90.5 - - - +
522S GLN* 1.3 65.2 + - - +
523S PRO* 3.1 5.6 - - - -
524S CYS* 3.0 13.5 + - + +
525S ILE* 2.9 17.6 + - + +
586S TYR* 3.8 24.5 - - + -
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Residues in contact with GLN 522 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488S LYS* 4.7 4.5 + - - +
491S GLN* 3.7 29.7 + - - +
495S HIS* 5.7 3.8 + - - -
520S ASP* 2.5 27.9 + - - +
521S LEU* 1.3 70.3 - - - +
523S PRO* 1.3 58.2 - - + +
525S ILE* 2.6 48.1 + - - +
526S GLU* 2.9 35.0 + - + +
529S GLU* 4.2 5.7 - - - +
675S ARG* 6.2 0.2 - - - +
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Residues in contact with PRO 523 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520S ASP* 3.0 17.5 - - + +
521S LEU* 4.0 5.8 - - - -
522S GLN* 1.3 90.6 - - + +
524S CYS* 1.3 55.5 + - - +
525S ILE 2.5 13.2 + - - -
526S GLU* 2.7 23.8 + - + +
527S LEU 3.1 9.4 + - - -
566S HIS* 3.8 19.2 + - + -
567S ALA* 6.2 1.8 - - + -
568S LYS* 4.6 8.7 - - + +
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Residues in contact with CYS 524 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487S GLU* 3.3 28.2 - - - +
521S LEU* 3.0 11.1 + - + +
523S PRO* 1.3 76.1 - - - +
525S ILE* 1.3 57.2 + - - +
527S LEU* 4.2 6.8 - - - +
528S ILE* 3.2 19.5 - - - +
568S LYS* 3.7 27.7 - - + +
583S ILE* 4.9 6.1 - - - -
584S LEU 3.4 25.4 - - - -
585S HIS* 3.7 22.4 - - - -
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Residues in contact with ILE 525 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484S TYR* 3.5 29.4 - - + -
487S GLU* 4.9 7.6 - - + +
488S LYS* 4.2 22.9 - - + +
491S GLN* 4.3 15.9 - - + -
521S LEU* 2.9 23.6 - - + +
522S GLN* 2.6 39.5 + - - +
523S PRO 2.5 5.3 + - - -
524S CYS* 1.3 72.1 - - - +
526S GLU* 1.3 58.1 + - - +
527S LEU 3.2 1.1 - - - -
528S ILE* 2.9 5.5 + - - +
529S GLU* 2.4 56.9 + - - +
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Residues in contact with GLU 526 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522S GLN* 3.2 36.4 - - + +
523S PRO* 2.7 16.4 + - + +
525S ILE* 1.3 76.2 - - - +
527S LEU* 1.3 52.7 + - - +
528S ILE 2.6 12.0 + - - -
529S GLU* 3.1 25.0 + - - +
530S ARG* 3.2 52.0 + - + +
534S PRO 4.9 0.8 - - - +
535S PRO 4.4 0.9 - - - +
536S GLY* 3.5 8.3 + - - -
566S HIS* 5.0 3.4 - - + +
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Residues in contact with LEU 527 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523S PRO 3.1 5.7 + - - +
524S CYS 4.2 8.7 - - - +
525S ILE 3.2 0.2 - - - -
526S GLU* 1.3 77.1 - - - +
528S ILE* 1.3 56.8 + - + +
535S PRO 4.9 0.2 - - - -
536S GLY* 3.5 3.1 - - - -
537S VAL* 2.8 37.3 + - + +
563S GLN* 3.6 18.7 - - + +
566S HIS* 3.1 48.5 + - + +
568S LYS* 3.3 33.2 - - + +
569S PHE* 3.5 11.9 - - + +
583S ILE* 3.5 19.3 - - + -
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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