Contacts of the helix formed by residues 21 - 28 (chain A) in PDB entry 1I4R
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 MET 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A SER* 3.9 28.3 - - - -
17A PHE* 3.6 12.7 - - + -
19A GLY 3.6 2.2 + - - -
20A THR* 1.3 72.1 - - - +
22A GLY* 1.3 56.8 + - - +
23A ASN 3.0 0.7 - - - -
24A MET* 2.9 25.8 + - - +
25A LYS* 3.1 9.0 + - - +
174A TYR* 4.1 24.5 - - + -
175A GLU 3.4 11.8 - - - +
176A PHE 3.2 4.0 + - - -
177A ASN 3.3 20.8 + - - +
178A SER* 3.4 22.7 - - - +
179A SER* 3.9 16.4 - - - +
201A MET* 4.2 2.7 - - - -
202A PRO* 3.9 35.4 - - + -
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Residues in contact with GLY 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 THR* 3.0 6.5 - - - +
21A MET* 1.3 76.9 - - - +
23A ASN* 1.3 60.7 + - - +
24A MET 3.2 0.2 - - - -
25A LYS* 3.6 10.8 - - - +
26A TYR* 3.0 27.5 + - - +
175A GLU 3.6 9.9 - - - -
176A PHE* 2.8 26.6 + - - -
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Residues in contact with ASN 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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20A THR* 3.0 31.5 + - - +
21A MET 3.0 1.0 - - - -
22A GLY* 1.3 78.3 - - - +
24A MET* 1.3 62.2 + - - +
26A TYR* 4.0 5.5 - - - +
27A LEU* 3.8 6.2 - - - +
176A PHE* 5.5 0.9 - - - -
208A PHE* 3.6 30.5 + - + +
210A GLN* 3.1 33.8 + - - +
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Residues in contact with MET 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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17A PHE* 6.2 0.4 - - + -
20A THR 4.3 0.2 + - - -
21A MET* 2.9 22.9 + - - +
23A ASN* 1.3 77.3 - - - +
25A LYS* 1.3 67.8 + - - +
27A LEU* 3.1 19.9 + - - +
28A TYR* 3.5 30.4 - - - -
174A TYR* 3.6 31.6 - - + -
200A MET 3.8 12.3 - - - +
202A PRO* 3.8 15.0 - - + -
208A PHE* 3.5 40.2 - - + -
213A TYR* 3.5 32.8 - - + -
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Residues in contact with LYS 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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21A MET 3.1 7.7 + - - +
22A GLY* 3.6 13.5 - - - +
24A MET* 1.3 77.9 - - - +
26A TYR* 1.3 58.2 + - - +
28A TYR* 3.1 3.5 + - - -
29A ASP* 2.9 57.8 + - + +
168A ILE* 3.9 17.2 - - + +
174A TYR* 3.5 47.6 + - + +
175A GLU* 4.3 13.0 - - - +
176A PHE* 4.8 2.5 - - - +
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Residues in contact with TYR 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 GLY 3.0 17.3 + - - +
23A ASN* 4.0 8.1 - - - +
24A MET 3.2 0.2 - - - -
25A LYS* 1.3 77.9 - - - +
27A LEU* 1.3 68.1 + - + +
29A ASP* 3.9 6.1 + - - +
31A HIS* 3.2 51.0 - + + +
88A ASN 4.5 2.7 - - - -
89A TYR* 5.3 1.1 - - - -
90A TYR* 3.4 33.8 - + - -
210A GLN* 3.5 26.9 - - - -
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Residues in contact with LEU 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 ASN 3.8 9.6 - - - +
24A MET* 3.1 10.6 + - - +
26A TYR* 1.3 82.5 - - + +
28A TYR* 1.3 72.2 + - + +
31A HIS* 3.3 14.1 - - - +
87A SER* 2.7 27.2 + - - +
88A ASN 3.7 22.9 - - - +
89A TYR* 4.6 1.3 - - + -
161A ILE* 5.0 0.2 - - - +
208A PHE* 4.0 29.2 - - + -
210A GLN* 3.9 25.6 - - + +
213A TYR* 4.5 5.4 - - + -
214A LEU* 3.9 35.2 - - + -
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Residues in contact with TYR 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 MET* 3.5 28.0 - - - -
25A LYS 3.1 2.4 + - - -
27A LEU* 1.3 92.7 - - + +
29A ASP* 1.3 58.9 + - - +
30A ASP 3.2 7.6 + - - -
31A HIS* 4.3 6.4 + - - -
87A SER* 5.2 0.9 - - - -
161A ILE* 3.7 37.3 - - + +
164A ARG* 3.4 50.2 + - + -
165A ASN* 3.2 22.1 + - - +
168A ILE* 3.7 18.2 - - + -
174A TYR* 4.2 6.1 - + - -
213A TYR* 3.4 20.9 - + - -
214A LEU* 4.2 3.5 - - + +
217A TYR* 2.7 35.7 + + - -
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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