Contacts of the helix formed by residues 24 - 29 (chain J) in PDB entry 1O1F
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 ARG 24 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4J ASP* 3.5 30.5 + - - +
7J MET* 5.9 1.2 - - - +
18J ARG* 4.7 25.1 - - - +
19J MLY 3.2 28.8 + - + +
20J SER 3.0 11.0 + - - +
21J GLU* 3.9 31.0 + - - +
23J GLU* 1.3 78.0 - - - +
25J ILE* 1.3 54.5 + - + +
27J ALA* 2.5 30.0 + - - +
28J GLN* 2.8 40.0 + - - +
87J MLY 5.6 3.4 - - - -
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Residues in contact with ILE 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J GLU* 2.8 35.0 - - + +
22J LYS* 3.0 12.5 + - + +
24J ARG* 1.3 85.4 - - + +
26J GLU* 1.3 62.0 + - + +
28J GLN* 4.6 3.1 - - - +
29J ASN* 3.0 45.6 + - + +
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Residues in contact with GLU 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J LYS* 2.3 78.7 + - + +
23J GLU* 4.0 9.2 + - - +
25J ILE* 1.3 69.3 - - + +
27J ALA* 1.3 58.5 + - - +
29J ASN 4.1 10.6 - - - +
30J MLY 4.2 10.6 - - - +
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Residues in contact with ALA 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J GLU 3.2 13.0 + - - +
24J ARG* 2.5 18.6 + - - +
26J GLU* 1.3 75.6 - - - +
28J GLN* 1.3 61.7 + - + +
29J ASN 3.3 1.1 - - - -
30J MLY 3.7 20.4 - - - +
83J PRO* 3.5 19.6 - - - +
86J ASP* 3.6 29.0 - - + +
87J MLY 4.3 11.2 - - - -
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Residues in contact with GLN 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ARG* 2.8 43.1 + - - +
25J ILE* 5.1 0.9 - - - -
27J ALA* 1.3 75.3 - - + +
29J ASN* 1.3 71.2 + - - +
30J MLY 3.5 4.4 + - - +
83J PRO* 3.6 28.5 - - - +
84J MLY 4.0 27.9 + - + +
86J ASP* 5.2 6.0 - - + +
719J ASP* 4.2 17.1 + - - +
722J GLN* 5.8 2.3 + - - -
723J ARG* 5.2 6.8 + - - -
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Residues in contact with ASN 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J ILE* 3.0 50.2 + - + +
26J GLU* 4.1 5.2 - - - +
28J GLN* 1.3 83.6 + - - +
30J MLY 1.3 61.4 + - - +
722J GLN* 3.4 32.3 + - - +
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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