Contacts of the helix formed by residues 535 - 540 (chain C) in PDB entry 4OIO
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 535 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C ILE* 5.0 0.8 - - - +
11C GLU* 2.8 37.6 + - - +
435C TYR* 5.7 0.2 + - - -
458C TYR* 4.0 19.3 - - - -
499C ALA* 4.2 6.1 - - - -
533C ASP* 4.6 3.8 - - - +
534C VAL* 1.3 81.4 - - - +
536C PRO* 1.3 75.4 - - - +
537C LYS* 3.4 15.7 + - - +
538C GLN* 3.1 22.7 + - - +
539C VAL* 4.9 0.9 - - - +
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Residues in contact with PRO 536 (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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9C ILE* 4.1 29.4 - - + -
11C GLU* 4.9 1.3 - - - +
499C ALA* 4.3 7.8 - - + -
500C ASN* 6.0 1.8 - - + +
535C SER* 1.3 91.1 - - - +
537C LYS* 1.3 63.8 + - + +
538C GLN 2.9 1.9 + - - -
539C VAL* 2.9 22.2 + - + +
540C PHE* 4.1 8.3 - - - -
905C ILE* 4.9 3.4 - - + -
906C PHE* 3.9 43.1 - - + +
907C ASP* 4.9 4.0 - - + +
1067D VAL* 4.6 18.8 - - + +
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Residues in contact with LYS 537 (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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11C GLU* 3.4 35.7 + - - -
15C LEU* 4.3 21.8 - - + -
457C ALA* 3.9 4.6 - - + +
458C TYR* 3.9 15.9 - - + +
535C SER* 3.1 8.9 - - - +
536C PRO* 1.3 79.8 - - + +
538C GLN* 1.3 59.9 + - - +
539C VAL 3.1 1.4 + - - -
540C PHE* 3.1 9.2 + - - +
545C ASN* 2.9 45.3 + - - +
581C THR 4.4 10.1 + - - -
582C GLY 6.1 0.8 - - - -
583C LEU* 5.1 11.5 - - + +
904C PRO* 4.2 22.0 - - - +
905C ILE* 4.8 10.9 - - + +
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Residues in contact with GLN 538 (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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435C TYR* 4.8 3.3 - - - -
436C GLY* 3.1 24.7 - - - +
456C ALA* 3.4 13.2 - - - +
458C TYR* 3.5 36.8 + - + +
469C THR* 2.5 31.9 + - - +
470C PRO* 3.3 14.8 + - - +
471C TYR* 4.1 10.4 + - - -
533C ASP* 3.7 9.5 - - + -
534C VAL* 2.9 33.1 + - - +
535C SER 3.1 20.2 + - - +
536C PRO 2.9 1.4 + - - -
537C LYS* 1.3 77.9 - - - +
539C VAL* 1.3 70.1 + - + +
540C PHE 3.3 0.2 - - - -
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Residues in contact with VAL 539 (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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435C TYR* 3.6 39.5 - - + +
436C GLY 4.2 10.5 + - - +
438C ILE 4.6 1.2 - - - +
439C CYS* 4.0 3.6 - - - -
440C PRO* 3.2 18.4 - - + +
456C ALA* 4.5 3.2 - - - +
535C SER 4.9 1.1 - - - +
536C PRO* 2.9 12.4 + - + +
538C GLN* 1.3 84.8 - - + +
540C PHE* 1.3 81.9 + - + +
1067D VAL* 3.6 20.0 - - + -
1071D PHE* 4.1 26.9 - - + -
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Residues in contact with PHE 540 (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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439C CYS* 3.9 4.7 - - - -
440C PRO* 3.8 19.7 - - + -
441C VAL* 3.6 26.5 - - + -
456C ALA* 4.2 1.6 - - - -
457C ALA 3.1 19.4 + - - -
536C PRO 4.1 11.2 - - - -
537C LYS 3.1 4.6 + - - +
539C VAL* 1.3 102.3 - - + +
541C SER* 1.3 61.0 + - - +
544C THR* 3.8 17.0 - - + -
545C ASN* 2.9 25.6 + - - +
550C LEU* 4.0 11.0 - - + -
905C ILE* 4.5 7.6 - - + -
906C PHE* 3.3 37.7 - + - -
1067D VAL* 4.6 4.7 - - + -
1070D TYR* 3.9 22.2 - + + -
1071D PHE 5.6 0.7 - - - -
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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