Contacts of the helix formed by residues 55 - 59 (chain U) in PDB entry 1SC8
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 ALA 55 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U SER* 1.3 83.4 + - - +
56U THR* 1.3 65.1 + - - +
57U HIS* 4.1 4.3 - - - +
58U CYS* 3.3 16.3 + - - +
59U PHE* 3.2 19.2 - - - -
102U ASP* 3.5 29.6 - - - +
104U ALA* 3.7 3.6 - - - -
196U GLY* 3.7 22.2 - - - +
212U ILE* 4.1 4.7 - - + -
213U VAL 4.2 2.5 - - - +
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Residues in contact with THR 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55U ALA* 1.3 67.0 - - - +
57U HIS* 1.3 59.1 + - - +
58U CYS 2.9 11.4 + - - -
59U PHE* 3.0 13.2 + - - +
60U ILE* 3.1 18.4 + - + -
90U LEU* 3.6 21.9 - - + +
91U HIS* 3.1 13.7 + - - +
94U TYR* 3.7 34.1 - - + -
101U ASN 4.4 1.3 - - - -
102U ASP* 3.1 5.8 + - - -
103U ILE 2.4 37.3 + - - +
104U ALA* 3.5 11.0 - - - +
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Residues in contact with HIS 57 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55U ALA* 3.3 5.6 - - + +
56U THR* 1.3 72.8 - - - +
58U CYS* 1.3 62.2 + - - +
59U PHE 3.3 0.6 + - - -
60U ILE* 3.9 18.1 + - + +
94U TYR* 3.2 30.7 - - + +
99U HIS* 4.0 8.8 + + + +
102U ASP* 2.5 45.2 + - - +
195U SER* 3.3 21.8 + - - -
214U SER* 3.4 22.0 + - - -
300U 2IN 4.1 10.2 - - - -
402U SO4 2.7 28.3 + - - -
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Residues in contact with CYS 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41U VAL* 3.6 17.4 - - + +
42U CYS* 2.0 54.1 - - + -
54U SER* 4.4 1.8 - - - -
55U ALA* 3.4 24.5 - - - +
56U THR 2.9 1.0 + - - -
57U HIS* 1.3 82.9 - - - +
59U PHE* 1.3 71.4 + - + +
60U TYR* 5.9 1.7 - - - +
64U TYR* 4.4 2.9 + - - -
195U SER* 3.9 15.7 - - - -
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Residues in contact with PHE 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U ILE* 3.9 36.1 - - + -
41U VAL* 4.5 3.6 - - + -
42U CYS* 5.1 0.7 - - + -
54U SER* 4.0 7.4 - - - -
55U ALA 3.2 24.7 - - - -
56U THR 3.0 1.8 + - - -
58U CYS* 1.3 93.5 - - + +
60U ILE* 1.3 95.4 + - - +
64U TYR* 3.7 35.9 - + - +
88U LEU* 4.0 18.8 - - + -
90U LEU* 4.0 27.1 - - + -
104U ALA* 4.2 2.2 - - + -
106U LEU* 3.8 32.1 - - + -
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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