Contacts of the helix formed by residues 445 - 452 (chain C) in PDB entry 5CO8
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 GLU 445 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368C ARG* 3.6 32.2 + - - -
378C PRO* 2.7 30.7 + - + +
380C LEU* 3.9 28.7 - - + +
443C VAL 3.3 5.3 + - - -
444C PRO* 1.3 71.8 - - - +
446C THR* 1.3 56.7 + - - +
448C LEU* 3.1 7.9 + - - +
449C LYS* 2.9 60.0 + - + +
456C VAL* 5.0 0.3 - - - +
460C GLU* 3.9 8.8 - - - +
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Residues in contact with THR 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 3.6 16.3 - - + +
26C LEU* 4.1 22.2 - - + -
27C GLU* 2.4 46.2 + - + -
444C PRO* 3.2 0.8 - - - +
445C GLU* 1.3 78.5 + - - +
447C ILE* 1.3 63.1 + - - +
449C LYS* 3.3 10.8 + - - +
450C LEU* 3.2 32.4 + - + +
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Residues in contact with ILE 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 3.8 27.1 - - + -
26C LEU* 4.1 14.8 - - + -
69C SER 4.5 2.2 - - - +
70C LEU 4.4 11.9 - - - +
335C VAL* 3.7 28.7 - - + -
338C CYS* 3.1 33.6 - - + +
339C LEU* 4.3 17.0 - - + -
443C VAL* 4.2 11.7 - - + -
444C PRO* 3.1 21.4 + - + +
446C THR* 1.3 77.5 - - - +
448C LEU* 1.3 62.7 + - - +
450C LEU* 3.2 9.1 + - - +
451C GLY 3.2 9.7 + - - -
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Residues in contact with LEU 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C LEU* 6.0 2.5 - - + -
338C CYS* 4.1 9.4 - - - -
362C VAL* 4.5 5.6 - - + -
365C ILE* 4.9 4.5 - - + -
380C LEU* 3.5 37.0 - - + +
382C VAL* 3.6 28.0 - - + -
443C VAL* 3.7 30.1 - - + +
444C PRO 3.6 8.7 - - - +
445C GLU* 3.1 8.4 + - - +
447C ILE* 1.3 75.5 - - - +
449C LYS* 1.3 60.3 + - - +
452C VAL* 2.9 50.1 + - + +
456C VAL* 3.7 13.2 - - + -
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Residues in contact with LYS 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C GLU* 2.9 44.7 + - + +
446C THR* 3.7 11.2 - - - +
447C ILE 3.3 0.2 - - - -
448C LEU* 1.3 76.5 - - - +
450C LEU* 1.3 67.2 + - + +
453C PRO* 3.3 26.0 - - - +
456C VAL* 4.1 20.4 - - + +
460C GLU* 2.8 30.7 + - - -
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Residues in contact with LEU 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 4.0 25.6 - - + +
338C CYS 4.3 4.7 - - - +
339C LEU* 3.9 24.9 - - + -
341C ARG* 5.2 1.2 - - - +
342C TYR* 3.9 52.1 - - + +
446C THR* 3.2 25.1 - - + +
447C ILE* 3.2 9.1 + - - +
448C LEU 3.1 0.6 - - - -
449C LYS* 1.3 88.2 - - + +
451C GLY* 1.3 59.1 + - - +
453C PRO* 4.3 4.9 - - - +
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Residues in contact with GLY 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C CYS* 3.2 31.2 + - - -
341C ARG* 3.3 33.0 + - - +
361C LEU* 5.2 0.2 - - - -
447C ILE 3.2 6.7 + - - -
450C LEU* 1.3 78.5 - - - +
452C VAL* 1.3 61.3 + - - +
453C PRO* 3.2 12.1 - - - +
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Residues in contact with VAL 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C CYS* 4.6 2.9 - - - -
341C ARG* 4.6 3.8 - - - +
358C GLU 4.4 13.5 - - - +
361C LEU* 4.2 29.8 - - + -
362C VAL* 4.1 18.4 - - + +
365C ILE* 6.0 0.9 - - + -
382C VAL* 6.0 0.2 - - + -
448C LEU* 2.9 40.5 + - + +
451C GLY* 1.3 76.9 - - - +
453C PRO* 1.3 64.8 - - - +
454C VAL 3.3 2.0 - - - -
455C THR* 3.3 20.2 + - + +
456C VAL* 3.2 19.7 + - + +
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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