Contacts of the helix formed by residues 21 - 31 (chain A) in PDB entry 3ESF
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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12A TYR 4.5 0.4 - - - -
16A ALA* 4.3 9.4 - - - +
19A GLY 4.1 0.6 - - - -
20A ILE* 1.3 75.9 - - - +
22A LYS* 1.3 65.4 + - - +
23A GLU* 3.5 9.4 + - - +
24A GLN 3.0 15.8 + - - -
25A VAL* 2.9 24.2 + - - +
169A ILE* 4.5 0.7 - - - +
170A ASP* 2.6 34.9 + - - -
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Residues in contact with LYS 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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12A TYR* 3.5 28.5 + - + +
13A ASP* 3.9 26.5 - - + +
16A ALA* 4.3 9.3 - - + +
20A ILE 3.9 0.2 + - - -
21A SER* 1.3 72.8 - - - +
23A GLU* 1.3 55.5 + - - +
25A VAL* 3.5 1.2 + - - +
26A THR* 2.7 43.2 + - - +
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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* 3.2 8.0 + - - +
22A LYS* 1.3 78.5 - - - +
24A GLN* 1.3 62.1 + - - +
26A THR* 3.4 5.4 + - - -
27A PHE* 3.1 50.8 + - + -
169A ILE* 3.6 20.2 - - + +
172B LYS* 3.9 15.6 + - - -
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Residues in contact with GLN 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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20A ILE* 3.9 11.2 - - + -
21A SER* 3.0 13.8 + - - +
23A GLU* 1.3 76.7 - - - +
25A VAL* 1.3 61.3 + - - +
27A PHE* 3.7 0.3 + - - -
28A HIS* 3.1 23.2 + - + +
165A HIS 2.9 25.1 + - - -
166A ALA* 3.2 19.7 + - - +
167A TYR* 3.0 13.6 - - - -
169A ILE* 2.9 45.7 + - + +
170A ASP* 3.2 33.9 + - + +
171A TYR* 6.3 0.2 - - + -
168B TYR* 5.3 0.4 + - - -
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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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8A LEU* 3.5 35.0 - - + -
10A TRP* 3.9 23.8 - - + -
12A TYR* 3.4 23.6 - - - +
15A LEU* 4.9 2.2 - - + -
20A ILE* 3.5 29.6 - - + +
21A SER 2.9 19.0 + - - +
24A GLN* 1.3 70.0 - - - +
26A THR* 1.3 60.2 + - - +
28A HIS* 3.9 4.2 - - - +
29A TYR* 2.9 30.0 + - - +
80A TRP* 4.4 9.0 - - + -
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Residues in contact with THR 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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12A TYR* 3.5 25.5 - - + +
22A LYS* 2.7 36.0 + - - +
23A GLU* 3.7 6.9 - - - -
24A GLN 3.3 0.2 - - - -
25A VAL* 1.3 70.2 - - - +
27A PHE* 1.3 66.6 + - + +
30A ASP* 2.7 57.5 + - + +
31A LYS* 5.7 5.2 - - - +
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Residues in contact with PHE 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 42.9 + - + +
24A GLN* 5.4 0.4 - - - +
26A THR* 1.3 85.1 - - + +
28A HIS* 1.3 59.3 + - - +
31A LYS* 2.9 61.6 + - + +
32A HIS* 3.3 5.4 + - - -
169A ILE* 3.7 26.2 - - + -
168B TYR* 4.1 9.4 - - - +
172B LYS* 3.8 32.8 - - + -
173B ASN* 3.6 22.0 - - - -
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Residues in contact with HIS 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 GLN* 3.1 25.4 + - - +
25A VAL 3.9 0.2 - - - +
26A THR 3.2 0.2 - - - -
27A PHE* 1.3 78.6 - - - +
29A TYR* 1.3 57.8 + - - +
32A HIS* 3.4 10.4 + - + +
33A HIS* 2.8 26.7 + - - +
76A HIS* 3.2 10.7 + + - -
79A TYR* 3.5 26.6 + + - -
80A TRP* 3.4 20.6 - + + -
161A ASP* 2.9 16.4 + - - -
165A HIS* 3.1 18.1 + + - +
166A ALA* 3.6 23.2 + - + -
198A FE 2.2 26.9 - - - -
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Residues in contact with TYR 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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5A ILE* 3.5 30.4 + - + +
6A PRO 2.7 30.3 + - - -
7A PRO* 3.4 8.2 - - + +
8A LEU* 3.5 32.8 - - + -
12A TYR* 3.8 17.3 - + + -
25A VAL 2.9 18.3 + - - +
26A THR 4.4 0.2 - - - +
28A HIS* 1.3 77.1 - - - +
30A ASP* 1.3 73.4 + - - +
33A HIS* 3.4 12.8 - + - +
34A MET* 2.9 37.7 + - + +
80A TRP* 3.4 31.6 - + + -
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Residues in contact with ASP 30 (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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12A TYR* 2.5 34.8 + - - -
26A THR* 2.7 42.1 + - + +
29A TYR* 1.3 80.8 - - - +
31A LYS* 1.3 70.4 + - + +
34A MET* 3.4 21.7 - - - +
35A GLY 4.4 0.5 + - - -
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Residues in contact with LYS 31 (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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26A THR* 5.7 4.4 - - - +
27A PHE* 2.9 46.3 + - + +
30A ASP* 1.3 87.7 - - + +
32A HIS* 1.3 60.1 + - + +
35A GLY* 2.9 27.5 + - - -
173B ASN* 3.6 44.9 - - + +
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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