Contacts of the helix formed by residues 601 - 608 (chain A) in PDB entry 4Y5U
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 SER 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A TYR* 3.9 11.6 + - - -
597A LEU* 3.3 13.5 + - - -
600A ARG* 1.3 78.6 - - - +
602A LEU* 1.3 60.4 + - - +
603A GLY* 3.6 2.6 + - - -
604A ASP* 3.1 28.5 + - - +
605A ARG* 3.0 26.2 + - - +
607A ARG* 5.5 0.7 + - - -
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Residues in contact with LEU 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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529A LEU* 4.0 12.1 - - + -
532A TYR* 3.9 37.1 + - + -
538A ILE* 5.2 0.7 - - + -
561A LEU* 4.1 31.6 - - + -
571A ILE* 4.2 13.2 - - + -
573A ILE* 5.0 0.9 - - + -
592A PHE* 4.1 28.5 - - + -
597A LEU* 3.5 23.0 - - + +
601A SER* 1.3 75.2 - - - +
603A GLY* 1.3 61.9 + - - +
605A ARG* 3.5 4.1 + - - +
606A ILE* 3.1 40.7 + - + +
625A PHE* 5.2 0.7 - - + -
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Residues in contact with GLY 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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532A TYR* 3.0 23.7 + - - -
601A SER* 3.2 1.1 - - - -
602A LEU* 1.3 77.0 - - - +
604A ASP* 1.3 59.5 + - - +
606A ILE* 3.5 2.6 + - - +
607A ARG* 3.2 44.0 + - - +
625A PHE* 4.5 17.8 - - - +
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Residues in contact with ASP 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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600A ARG* 3.5 35.6 + - + +
601A SER* 3.1 25.4 + - - +
603A GLY* 1.3 75.2 - - - +
605A ARG* 1.3 62.1 + - - +
607A ARG* 3.5 23.8 + - - +
608A ASP* 3.1 27.4 + - - +
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Residues in contact with ARG 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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573A ILE* 5.8 0.9 - - + -
592A PHE* 3.4 42.4 - - + -
596A ASP* 2.6 44.0 + - - +
597A LEU* 4.1 7.0 - - - +
599A ILE* 4.6 4.8 - - - +
600A ARG* 3.3 29.7 + - + +
601A SER 3.0 16.1 + - - +
602A LEU* 3.8 4.5 - - - +
604A ASP* 1.3 76.2 - - - +
606A ILE* 1.3 61.4 + - + +
608A ASP* 3.3 20.7 + - - +
609A LEU* 3.8 4.3 + - - +
648A MET* 3.6 39.2 - - + +
644B ALA* 5.8 1.2 - - - +
645B THR 5.8 0.4 - - - -
646B ILE* 3.8 28.3 - - - +
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Residues in contact with ILE 606 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A PHE* 3.8 26.2 - - + -
561A LEU* 4.3 12.1 - - + -
573A ILE* 4.4 13.7 - - + -
602A LEU* 3.1 41.4 + - + +
603A GLY* 3.9 4.5 - - - +
604A ASP 3.4 0.2 - - - -
605A ARG* 1.3 73.7 - - + +
607A ARG* 1.3 64.5 + - + +
609A LEU* 3.3 14.0 + - - +
612A LEU* 3.8 18.4 - - + +
621A LYS* 3.5 28.5 + - + -
625A PHE* 3.7 34.3 - - + -
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Residues in contact with ARG 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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601A SER* 5.5 0.6 + - - -
603A GLY* 3.2 29.3 + - - +
604A ASP* 3.7 25.6 + - - +
606A ILE* 1.3 71.9 - - - +
608A ASP* 1.3 58.1 + - - +
609A LEU 2.9 11.6 + - - -
610A ALA* 5.3 0.5 - - - -
621A LYS* 4.0 22.8 + - + +
622A ASP* 5.2 6.3 - - - +
625A PHE* 3.9 24.2 + - + +
626A ARG* 3.7 34.1 - - - +
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Residues in contact with ASP 608 (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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600A ARG* 2.6 42.6 + - - -
604A ASP 3.1 16.0 + - - +
605A ARG* 3.3 12.1 - - - +
606A ILE 3.1 0.2 - - - -
607A ARG* 1.3 77.0 - - - +
609A LEU* 1.3 62.3 + - - +
610A ALA* 3.8 2.3 + - - +
647A LYS* 3.5 28.3 - - + +
648A MET* 3.2 31.6 + - - +
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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