Contacts of the helix formed by residues 577 - 583 (chain A) in PDB entry 2IUK
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 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571A SER 4.2 2.2 - - - -
572A LEU 4.1 1.3 - - - -
574A ASN* 3.6 28.7 + - - -
575A ALA 3.3 2.6 - - - -
576A ASP* 1.3 76.8 - - - +
578A ILE* 1.3 66.3 + - - -
579A ILE 3.6 1.8 - - - -
580A GLU* 3.5 4.0 + - - +
581A LYS* 3.1 31.4 + - - +
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Residues in contact with ILE 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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282A ILE* 4.9 4.0 - - + -
285A LEU* 4.0 4.9 - - + -
286A SER* 3.9 20.4 - - - +
290A ILE* 3.7 29.6 - - + -
571A SER 3.9 13.2 + - - +
572A LEU* 3.6 20.4 + - + -
577A GLY* 1.3 71.0 - - - +
579A ILE* 1.3 66.7 + - + +
581A LYS* 3.9 3.7 - - + +
582A SER* 3.1 29.7 + - - +
772A ILE* 3.9 14.1 - - + -
776A VAL* 3.6 46.7 - - + -
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Residues in contact with ILE 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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521A GLN* 3.8 23.3 - - + +
522A LEU* 3.7 29.6 - - + -
572A LEU* 3.0 35.1 + - + +
573A ILE* 3.9 18.8 - - + -
578A ILE* 1.3 80.1 - - + +
580A GLU* 1.3 56.9 + - + +
583A PHE* 3.0 55.6 + - + +
589A SER* 4.1 3.7 + - - +
590A ILE* 4.5 8.5 - - + -
776A VAL* 5.4 4.7 - - + -
780A LEU* 6.1 3.4 - - + -
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Residues in contact with GLU 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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227A ARG* 3.2 33.6 + - - +
572A LEU 5.2 1.3 - - - +
573A ILE 4.5 3.6 - - - +
574A ASN 3.6 21.4 - - - +
576A ASP* 3.6 10.4 + - - +
577A GLY 3.5 10.0 + - - +
578A ILE 3.4 0.6 - - - -
579A ILE* 1.3 75.9 - - + +
581A LYS* 1.3 65.9 + - - +
582A SER 3.5 0.2 - - - -
583A PHE 3.7 3.8 - - - +
586A GLY* 3.3 45.6 - - - +
587A LYS* 3.5 16.6 - - - +
589A SER* 4.3 4.2 - - - +
590A ILE* 4.3 17.1 - - + +
736A LEU* 5.5 0.2 - - - +
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Residues in contact with LYS 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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290A ILE* 4.8 12.8 - - + +
294A LYS* 6.2 0.9 - - - +
576A ASP* 3.4 43.8 + - - +
577A GLY* 3.1 23.7 + - - +
578A ILE* 3.9 5.6 - - + +
580A GLU* 1.3 80.1 - - - +
582A SER* 1.3 59.7 + - - +
736A LEU* 3.8 8.0 - - - +
768A PHE* 5.2 9.1 - - + -
769A GLU* 3.4 26.6 - - - +
772A ILE* 4.2 26.9 - - + -
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Residues in contact with SER 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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578A ILE* 3.1 13.9 + - - +
581A LYS* 1.3 77.8 - - - +
583A PHE* 1.3 74.0 + - - +
735A THR* 2.7 28.6 + - - -
736A LEU* 3.2 8.4 - - - +
769A GLU* 4.0 9.4 + - - -
772A ILE* 3.0 32.7 - - - +
773A ASP* 4.0 19.8 + - - -
776A VAL* 6.2 0.4 - - - -
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Residues in contact with PHE 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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517A SER* 3.6 34.5 - - - -
518A GLY* 4.2 6.3 - - - -
521A GLN* 3.6 24.2 - - + -
522A LEU* 5.5 2.7 - - + -
579A ILE* 3.0 56.6 + - + +
580A GLU 3.7 6.9 - - - +
581A LYS 3.7 0.2 - - - -
582A SER* 1.3 89.9 - - - +
584A LEU* 1.3 67.8 + - - +
585A PRO* 3.6 10.3 - - + -
586A GLY* 3.3 9.4 + - - -
589A SER* 4.6 2.2 - - - +
735A THR* 3.8 24.7 - - + -
736A LEU* 3.4 10.2 - - - +
773A ASP* 3.9 18.4 - - - -
776A VAL* 6.2 2.0 - - + -
777A ILE* 5.3 3.6 - - + -
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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