Contacts of the helix formed by residues 20 - 28 (chain A) in PDB entry 4YET
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 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A MET 4.4 1.1 - - - -
16A ILE* 4.3 8.1 - - - -
17A PRO 5.5 0.6 - - - -
19A ILE* 1.3 76.3 - - - +
21A GLU* 1.3 64.1 + - - +
22A GLU* 3.5 9.4 + - - +
23A THR* 3.0 18.5 + - - -
24A LEU* 3.1 23.0 + - - +
166A ILE* 4.3 0.2 - - - +
167A ASP* 2.6 35.6 + - - -
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Residues in contact with GLU 21 (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 MET* 3.3 31.3 + - + +
13A ARG* 2.9 53.4 + - + +
16A ILE* 4.2 11.2 - - + +
19A ILE 4.0 0.2 + - - -
20A SER* 1.3 73.6 - - - +
22A GLU* 1.3 62.7 + - - +
24A LEU* 3.3 3.6 + - - +
25A SER* 2.9 24.2 + - - -
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Residues in contact with GLU 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 SER* 3.2 9.4 + - - +
21A GLU* 1.3 78.3 - - - +
23A THR* 1.3 64.2 + - - +
25A SER* 2.7 24.4 + - - +
26A PHE* 3.1 30.6 + - + -
166A ILE* 3.7 22.0 - - + +
169B LYS* 3.1 26.6 + - - -
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Residues in contact with THR 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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19A ILE* 3.6 18.4 - - + -
20A SER* 3.0 11.6 + - - -
22A GLU* 1.3 76.5 - - - +
24A LEU* 1.3 59.2 + - + +
26A PHE* 3.3 1.6 + - - +
27A HIS* 2.7 46.3 + - + +
162A HIS 4.6 4.3 - - - +
163A ALA 3.7 24.6 + - - +
164A TYR 5.6 0.6 - - - -
166A ILE* 3.6 21.2 + - + +
167A ASP* 2.6 33.8 + - - +
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Residues in contact with LEU 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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8A LEU* 4.3 8.5 - - + -
10A TYR* 4.3 9.9 - - + -
11A GLY 4.4 0.2 - - - +
12A MET* 3.6 44.0 - - + +
15A LEU* 3.9 31.4 - - + -
19A ILE* 3.9 17.0 - - + -
20A SER 3.1 11.0 + - - +
21A GLU 3.3 5.8 + - - +
23A THR* 1.3 78.3 - - + +
25A SER* 1.3 59.4 + - - +
27A HIS* 4.4 0.4 - - - +
28A TYR* 2.9 35.1 + - - +
78A TRP* 3.5 34.1 - - + -
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Residues in contact with SER 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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12A MET* 3.9 17.2 - - - -
21A GLU* 2.9 17.3 + - - -
22A GLU* 2.7 24.1 + - - +
24A LEU* 1.3 76.4 - - - +
26A PHE* 1.3 68.7 + - - +
29A GLY* 3.1 25.3 + - - -
30A LYS* 3.6 7.5 + - - +
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Residues in contact with PHE 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 GLU* 3.1 34.3 + - + +
23A THR 4.0 1.6 - - - +
25A SER* 1.3 88.8 + - - +
27A HIS* 1.3 62.3 + - - +
30A LYS* 3.0 28.7 + - + +
31A HIS* 2.9 28.8 + - + -
166A ILE* 3.9 16.8 - - + -
165B TYR* 3.8 14.4 - - - +
169B LYS* 3.5 47.1 - - + -
170B ASN* 3.5 22.7 - - - -
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Residues in contact with HIS 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 THR* 2.7 31.6 + - + +
24A LEU 4.5 0.2 - - - +
26A PHE* 1.3 73.6 - - - +
28A TYR* 1.3 57.9 + - - +
31A HIS* 3.4 9.4 - - + +
32A HIS* 3.0 26.0 + - - +
74A HIS* 3.2 13.5 + + - -
77A TYR* 3.6 23.4 + + - -
78A TRP* 3.5 17.6 - + + -
158A ASP* 2.9 17.7 + - - -
162A HIS* 3.1 19.0 + + - +
163A ALA* 3.6 26.3 + - + +
300A FE 2.2 26.6 - - - -
165B TYR* 5.4 0.2 - - - -
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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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5A LEU* 3.5 33.6 + - + +
6A PRO 2.7 28.7 + - - -
7A ALA* 3.4 11.6 - - - -
8A LEU* 3.5 34.0 + - + -
12A MET* 3.5 24.7 - - + -
24A LEU* 2.9 16.0 + - - +
27A HIS* 1.3 79.3 - - - +
29A GLY* 1.3 60.5 + - - +
30A LYS 3.4 0.2 + - - -
32A HIS* 3.4 10.5 - - - +
33A ALA* 3.1 27.9 + - - +
78A TRP* 3.5 34.7 - + + -
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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