Contacts of the helix formed by residues 54 - 59 (chain K) in PDB entry 6AHU
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 ASP 54 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C SER* 4.9 0.2 - - - -
25C LEU 3.5 8.6 + - - +
26C ASN* 3.3 22.7 + - + +
27C ASN* 2.9 29.6 + - - +
28C PRO* 4.0 3.0 - - + +
53K ARG* 1.3 77.3 - - - +
55K PRO* 1.3 71.5 - - + +
56K SER* 3.1 25.0 + - - +
57K VAL* 3.3 21.4 - - - +
58K LYS* 3.3 21.6 + - - +
118K LEU* 6.2 1.3 - - + -
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Residues in contact with PRO 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A U 5.2 1.1 - - - +
242A U 3.9 23.2 + - - +
243A G 3.4 36.1 - - - +
53K ARG 4.1 0.2 - - - +
54K ASP* 1.3 85.3 - - + +
56K SER* 1.3 63.2 + - - +
58K LYS* 4.0 8.5 - - + -
59K ARG* 3.3 28.1 + - - +
114K PRO* 4.9 12.6 - - + +
115K GLU* 4.4 20.6 - - + +
118K LEU* 6.0 5.2 - - + -
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Residues in contact with SER 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PRO* 4.0 18.5 - - - +
54K ASP* 3.1 19.7 + - - +
55K PRO* 1.3 80.8 - - - +
57K VAL* 1.3 66.1 + - - +
59K ARG* 3.3 30.5 + - - +
60K THR* 3.9 8.5 - - - +
115K GLU* 3.4 26.0 + - - -
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Residues in contact with VAL 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASN* 3.4 25.6 - - + +
28C PRO* 5.4 0.2 - - + -
207C TRP* 5.2 6.5 - - + -
18K TYR* 3.6 40.8 - - + +
42K GLU* 5.4 1.8 - - - +
53K ARG* 6.2 0.4 - - + -
54K ASP* 3.3 30.7 + - - +
56K SER* 1.3 81.0 + - - +
58K LYS* 1.3 58.1 + - - +
59K ARG 3.2 0.4 - - - -
60K THR* 2.4 33.4 + - - -
61K LEU* 3.3 10.1 - - + +
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Residues in contact with LYS 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A U 4.1 8.7 + - - -
243A G 3.0 58.4 + - - -
244A G 5.3 5.6 - - - -
53K ARG* 3.4 45.9 - - + +
54K ASP 3.3 17.0 + - - +
55K PRO* 4.3 6.3 - - + -
56K SER 3.5 0.2 - - - -
57K VAL* 1.3 77.5 - - - +
59K ARG* 1.3 61.1 + - - +
60K THR 3.2 1.5 + - - -
61K LEU* 3.4 24.0 + - + +
62K CYS 4.3 2.8 + - - -
63K ARG* 3.1 31.0 + - + +
99K GLN* 4.9 3.1 + - - -
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Residues in contact with ARG 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A U 4.6 8.3 + - - -
242A U 5.0 2.0 - - - +
142C MET* 5.1 4.2 + - - +
143C ILE* 3.4 50.9 - - - +
55K PRO 3.3 18.7 + - - +
56K SER* 3.3 23.7 + - - +
58K LYS* 1.3 78.8 - - - +
60K THR* 1.3 62.1 + - + +
61K LEU 3.6 0.2 - - - -
62K CYS* 4.6 1.0 + - - +
63K ARG* 5.6 1.6 - - - +
90K GLN* 3.0 23.0 - - - +
99K GLN* 3.0 25.3 + - - +
101K PHE* 3.6 40.1 - - + -
115K GLU* 3.8 26.8 + - - -
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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