Contacts of the helix formed by residues 574 - 583 (chain A) in PDB entry 4I1R
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 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A LYS* 5.0 5.6 - - - +
573A SER* 1.4 76.6 - - - +
575A VAL* 1.4 60.8 + - + +
576A ARG 3.3 2.5 - - - +
577A ASN* 3.3 29.3 - - + +
578A LEU* 3.8 5.0 + - - +
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Residues in contact with VAL 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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573A SER* 3.1 18.8 - - - +
574A LEU* 1.4 76.3 - - + +
576A ARG* 1.4 58.6 + - - +
577A ASN 3.2 0.9 - - - -
578A LEU* 3.2 27.7 + - + +
579A GLN* 3.3 22.2 + - - +
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Residues in contact with ARG 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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342A ASP* 3.5 26.9 - - - +
344A VAL* 4.5 3.1 - - + -
379A LYS* 4.3 3.0 - - + +
400A LEU 5.4 2.8 + - - -
401A LEU* 3.5 32.9 - - + +
403A ASP* 5.0 8.3 + - - -
573A SER 3.8 10.4 + - - +
574A LEU 3.3 0.2 - - - -
575A VAL* 1.4 75.8 - - - +
577A ASN* 1.4 61.1 + - - +
579A GLN* 2.7 33.5 + - - +
580A TRP* 3.2 17.2 + - - +
801A LZU 3.3 59.5 - - + +
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Residues in contact with ASN 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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379A LYS* 3.5 40.4 - - - +
574A LEU* 3.3 21.5 + - + +
575A VAL 3.2 0.6 - - - -
576A ARG* 1.4 77.2 - - - +
578A LEU* 1.3 60.5 + - - +
580A TRP* 3.5 8.0 + - - +
581A ALA* 3.3 21.3 + - - +
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Residues in contact with LEU 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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574A LEU 3.8 5.0 + - - +
575A VAL* 3.2 18.9 + - + +
577A ASN* 1.3 78.3 - - - +
579A GLN* 1.4 57.1 - - - +
581A ALA* 3.6 10.3 + - + +
582A LYS* 3.3 28.0 + - + +
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Residues in contact with GLN 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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575A VAL* 3.3 22.0 + - - +
576A ARG* 2.7 48.5 + - - +
577A ASN 3.4 0.2 - - - -
578A LEU* 1.4 75.0 - - - +
580A TRP* 1.4 61.3 + - - +
582A LYS* 3.5 14.7 - - + +
583A ALA* 3.2 22.0 + - - +
715A LEU* 5.3 1.6 - - - +
801A LZU 4.4 22.2 - - + +
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Residues in contact with TRP 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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374A ARG* 3.7 39.9 - - + -
378A PHE 5.7 0.4 - - - -
379A LYS* 3.6 30.1 - - + -
380A VAL 2.6 34.5 + - - +
381A VAL* 4.8 1.3 - - + -
576A ARG 3.2 7.2 + - - +
577A ASN* 3.6 13.2 - - - +
579A GLN* 1.4 74.1 - - - +
581A ALA* 1.4 71.7 + - + +
583A ALA* 3.1 18.1 + - + +
584A HIS* 3.2 49.1 + + + -
801A LZU 3.6 29.1 - + + +
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Residues in contact with ALA 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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577A ASN* 3.3 12.3 + - - +
578A LEU* 3.7 18.6 - - + +
579A GLN 3.5 0.4 - - - -
580A TRP* 1.4 90.9 - - + +
582A LYS* 1.4 60.2 + - - +
584A HIS* 3.2 12.8 + - - +
585A GLU* 3.4 18.7 + - - +
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Residues in contact with LYS 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 LEU* 3.3 13.5 + - + +
579A GLN* 3.5 19.3 - - + +
581A ALA* 1.4 76.7 - - - +
583A ALA* 1.3 60.8 + - - +
584A HIS 3.4 1.0 + - - -
585A GLU* 3.9 15.7 + - - +
711A LEU 4.8 0.3 - - - +
714A LYS* 3.2 59.0 + - + +
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Residues in contact with ALA 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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381A VAL* 5.7 3.1 - - + -
579A GLN 3.2 10.5 + - - +
580A TRP* 3.1 14.7 + - + +
582A LYS* 1.3 79.3 - - - +
584A HIS* 1.4 69.6 + - + +
585A GLU 3.7 1.1 - - - -
711A LEU 3.0 28.0 - - - -
712A ILE* 3.3 8.0 + - + -
714A LYS* 5.1 1.6 - - - -
715A LEU* 3.6 28.9 - - + +
801A LZU 5.5 7.2 - - + -
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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