Contacts of the helix formed by residues 601 - 607 (chain A) in PDB entry 4RA4
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 ASP 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599A ARG 3.5 5.4 + - - +
600A ILE* 1.3 70.8 - - - +
602A TRP* 1.3 52.9 + - - +
603A GLU* 3.8 7.8 + - - +
604A LYS* 3.0 44.4 + - + +
605A LEU* 2.8 32.9 + - - +
610A ILE* 3.6 10.8 - - + +
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Residues in contact with TRP 602 (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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445A ALA* 3.9 16.2 - - + -
448A SER* 3.6 21.1 - - - -
449A ILE* 3.6 33.0 - - + -
452A PHE* 4.6 0.9 - + - -
591A VAL* 5.5 0.2 - - + -
592A ARG* 2.8 73.9 + - + +
597A PHE* 3.6 31.6 + + + +
600A ILE* 3.4 20.0 + - + +
601A ASP* 1.3 72.7 + - - +
603A GLU* 1.3 58.0 + - - +
605A LEU* 3.7 15.2 - - + +
606A GLU* 2.8 38.4 + - - +
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Residues in contact with GLU 603 (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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601A ASP* 3.3 8.9 + - - +
602A TRP* 1.3 79.4 - - - +
604A LYS* 1.3 60.3 + - - +
606A GLU* 3.9 9.1 - - - +
607A ASN* 3.0 46.7 + - - +
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Residues in contact with LYS 604 (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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601A ASP* 3.0 35.1 + - + +
603A GLU* 1.3 77.6 + - - +
605A LEU* 1.4 59.1 + - - +
607A ASN 3.6 1.6 + - - -
608A ARG 3.4 2.3 + - - -
609A GLU* 2.8 61.5 + - + +
610A ILE* 4.1 13.9 - - + -
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Residues in contact with LEU 605 (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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399A PHE* 3.5 11.1 - - - -
442A PHE* 4.3 20.4 - - + -
445A ALA* 3.5 30.1 - - + -
446A GLU* 4.0 11.9 - - + +
449A ILE* 3.4 32.1 - - + -
600A ILE* 3.8 32.8 - - + -
601A ASP 2.8 19.3 + - - +
602A TRP* 3.7 11.7 - - + +
603A GLU 3.4 0.2 - - - -
604A LYS* 1.4 69.2 - - - +
606A GLU* 1.4 56.1 + - - +
607A ASN 3.1 4.0 - - - -
608A ARG* 2.9 21.5 + - - -
610A ILE* 3.7 19.2 - - + +
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Residues in contact with GLU 606 (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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397A PRO* 5.4 0.7 - - - +
398A PRO* 4.1 12.6 - - - +
399A PHE* 3.9 19.7 - - - -
449A ILE* 3.7 26.6 - - + +
592A ARG* 2.7 29.9 + - - -
602A TRP* 2.8 28.4 + - - +
603A GLU* 3.9 8.0 + - - +
605A LEU* 1.4 74.8 - - - +
607A ASN* 1.3 71.7 + - - +
608A ARG 3.4 1.7 + - - -
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Residues in contact with ASN 607 (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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398A PRO* 5.4 3.3 - - - +
603A GLU* 3.0 35.9 + - - +
604A LYS 3.6 1.4 + - - +
605A LEU 3.1 1.2 - - - -
606A GLU* 1.3 87.5 + - - +
608A ARG* 1.4 64.4 + - - +
609A GLU* 3.1 36.3 + - - +
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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