Contacts of the helix formed by residues 603 - 613 (chain A) in PDB entry 5I73
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 THR 603 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A PRO 4.0 0.2 - - - +
602A GLY* 1.3 75.5 - - - +
604A PHE* 1.3 60.9 + - - +
605A LYS* 3.2 11.2 - - - -
606A GLU* 3.1 14.1 + - - +
607A ARG* 3.0 26.6 + - - +
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Residues in contact with PHE 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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602A GLY 4.0 0.4 + - - -
603A THR* 1.3 75.1 - - - +
605A LYS* 1.3 57.1 + - - +
607A ARG* 3.8 7.0 - - - +
608A ILE* 2.9 30.8 + - - +
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Residues in contact with LYS 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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603A THR* 3.2 7.5 - - - -
604A PHE* 1.3 79.0 - - - +
606A GLU* 1.3 57.6 + - - +
608A ILE* 3.8 6.1 - - - +
609A ILE* 2.9 27.5 + - - +
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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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601A PRO 4.9 3.6 - - - +
602A GLY* 4.8 2.7 - - - -
603A THR* 3.1 24.5 + - - +
605A LYS* 1.3 77.2 - - - +
607A ARG* 1.3 60.1 + - - +
609A ILE* 3.2 7.2 + - - +
610A LYS* 2.9 28.9 + - - +
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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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596A ARG* 5.1 3.6 - - + +
597A LEU* 4.8 17.9 - - + +
600A THR* 3.7 37.4 - - - +
601A PRO 4.5 2.4 + - - +
602A GLY 5.8 0.2 - - - +
603A THR 3.0 14.8 + - - +
604A PHE* 3.8 7.9 - - - +
606A GLU* 1.3 77.4 - - - +
608A ILE* 1.3 56.2 + - - +
610A LYS* 3.3 5.8 + - - +
611A SER* 2.9 27.1 + - - -
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Residues in contact with ILE 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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157A ILE* 5.7 1.3 - - + +
604A PHE 2.9 18.2 + - - +
605A LYS* 4.1 6.1 - - - +
607A ARG* 1.3 73.8 - - - +
609A ILE* 1.3 60.0 + - - +
611A SER* 3.5 9.2 - - - -
612A ILE* 2.9 30.3 + - - +
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Residues in contact with ILE 609 (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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605A LYS 2.9 20.9 + - - +
606A GLU* 3.4 10.1 - - - +
607A ARG 3.2 0.2 - - - -
608A ILE* 1.3 77.8 - - - +
610A LYS* 1.3 55.7 + - - +
611A SER 3.1 1.6 - - - -
612A ILE* 3.9 3.8 - - - +
613A THR* 3.0 32.7 + - - -
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Residues in contact with LYS 610 (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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156A PRO* 3.8 9.2 - - - +
596A ARG* 5.2 4.1 + - - -
600A THR* 5.7 5.4 - - - -
606A GLU 2.9 16.3 + - - +
607A ARG* 3.6 6.7 - - - +
608A ILE 3.3 0.2 - - - -
609A ILE* 1.3 75.9 - - - +
611A SER* 1.3 57.2 + - - +
612A ILE 3.4 0.2 - - - -
613A THR* 3.4 19.1 - - - +
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Residues in contact with SER 611 (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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155A CYS* 3.7 5.4 - - - +
156A PRO* 3.3 26.8 - - - +
157A ILE* 3.6 48.7 - - - +
515A PHE* 5.6 0.2 - - - -
596A ARG* 4.6 6.1 - - - -
607A ARG 2.9 16.6 + - - -
608A ILE* 3.5 10.8 - - - -
609A ILE 3.1 0.4 - - - -
610A LYS* 1.3 78.6 - - - +
612A ILE* 1.3 57.2 + - - +
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Residues in contact with ILE 612 (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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154A ILE 3.4 9.6 - - - +
155A CYS* 4.3 11.4 - - - -
157A ILE* 6.2 0.2 - - + -
515A PHE* 4.7 25.7 - - + +
516A TYR* 5.8 1.4 - - - -
608A ILE 2.9 16.1 + - - +
609A ILE* 3.4 4.9 + - - +
611A SER* 1.3 79.8 - - - +
613A THR* 1.3 59.9 + - - +
614A PRO* 3.3 11.4 - - - +
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Residues in contact with THR 613 (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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154A ILE 4.2 2.7 - - - +
156A PRO* 4.6 4.7 - - - +
609A ILE 3.0 18.4 + - - -
610A LYS* 3.4 18.4 - - - +
612A ILE* 1.3 75.6 + - - +
614A PRO* 1.3 78.8 - - - +
615A GLU* 4.7 0.5 - - - -
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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