Contacts of the helix formed by residues 21 - 29 (chain A) in PDB entry 4RN1
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A TYR* 1.3 88.4 - - - +
22A PRO* 1.3 70.1 - - - +
23A GLU* 3.6 12.0 + - - +
24A TYR* 2.9 43.8 + - - +
25A VAL 3.0 11.3 + - - -
58A LYS* 4.0 20.1 + - - +
59A PRO* 4.0 10.9 - - - +
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Residues in contact with PRO 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 3.7 27.1 - - + +
21A SER* 1.3 86.2 - - - +
23A GLU* 1.3 76.4 + - - +
25A VAL* 3.7 4.0 + - + +
26A SER* 3.3 24.1 + - - -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER* 3.6 11.1 + - - +
22A PRO* 1.3 96.4 - - - +
24A TYR* 1.3 64.0 + - - +
26A SER* 2.9 20.0 + - - -
27A MET* 3.1 14.0 + - - +
58A LYS* 3.7 17.6 + - - +
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.3 17.7 - - + -
20A TYR* 4.5 0.9 - - - -
21A SER* 2.9 28.7 + - - +
23A GLU* 1.3 74.9 - - - +
25A VAL* 1.3 67.9 + - + +
27A MET* 3.2 4.9 + - - +
28A CYS* 3.0 54.7 + - - -
59A PRO* 3.6 24.0 - - + -
114A ALA* 3.5 36.1 - - + -
115A ILE* 4.0 6.1 - - - +
118A ALA* 3.3 17.2 - - + +
136A ASN* 2.7 30.2 + - - -
138A SER* 3.3 18.2 - - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 3.5 36.8 - - + -
21A SER 3.0 9.1 + - - +
22A PRO* 4.0 4.7 - - + +
24A TYR* 1.3 83.7 - - + +
26A SER* 1.3 63.9 + - - +
28A CYS* 3.2 16.6 + - - +
29A ASP* 3.3 14.8 + - - +
38A ALA* 4.0 7.7 - - + +
39A ASP* 3.7 42.4 - - + +
42A HIS* 4.4 13.2 - - + -
138A SER* 5.6 2.0 - - - +
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO 3.3 12.9 + - - -
23A GLU* 2.9 21.0 + - - -
25A VAL* 1.3 81.8 - - - +
27A MET* 1.3 61.0 + - - +
29A ASP* 3.3 7.9 + - - +
30A SER* 3.2 20.6 + - - -
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU 3.1 16.0 + - - +
24A TYR* 3.5 7.0 - - - +
26A SER* 1.3 81.2 + - - +
28A CYS* 1.3 60.7 + - - +
30A SER* 2.5 38.2 + - - -
107A GLY 5.0 1.3 - - - +
110A ASP* 3.9 36.6 - - + +
111A TYR* 3.6 12.0 - - + -
114A ALA* 3.6 27.1 - - + -
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Residues in contact with CYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.0 56.5 + - - -
25A VAL* 3.2 10.0 + - - +
27A MET* 1.3 77.1 - - - +
29A ASP* 1.3 62.3 + - - +
30A SER 3.4 0.6 + - - -
31A LEU* 4.8 1.9 + - - +
38A ALA* 3.9 15.5 - - + -
111A TYR* 3.6 21.8 + - + -
114A ALA* 5.7 0.4 - - - -
115A ILE* 3.6 13.9 - - + -
138A SER* 3.5 17.5 - - - +
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Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.3 10.0 + - - +
26A SER* 3.3 6.9 + - - +
27A MET 3.1 0.6 - - - -
28A CYS* 1.3 77.9 - - - +
30A SER* 1.3 62.7 + - - +
31A LEU 3.2 3.4 - - - -
32A ALA* 3.1 20.9 + - - +
34A ILE 4.2 4.7 - - - +
36A LYS* 3.4 28.0 + - + +
37A ARG* 3.4 5.4 + - - +
38A ALA* 3.1 26.9 + - - +
39A ASP* 3.1 30.3 + - - +
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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