Contacts of the helix formed by residues 20 - 29 (chain A) in PDB entry 4KQS
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 HIS 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASP* 3.1 27.1 + - - +
17A PHE* 3.1 12.5 + - - +
18A VAL 3.1 0.8 - - - -
19A GLN* 1.3 79.6 + - + +
21A PHE* 1.4 63.0 + - - +
22A SER 3.3 1.6 - - - -
23A GLN* 3.3 14.4 + - - +
24A ILE* 3.2 21.1 + - - +
86A TRP* 3.2 75.1 + + + -
90A TRP* 4.2 4.3 - - - +
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Residues in contact with PHE 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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17A PHE 3.9 1.8 + - - -
18A VAL 3.0 17.3 + - - +
20A HIS* 1.4 78.0 - - - +
22A SER* 1.4 58.7 + - - +
24A ILE* 3.1 15.6 + - + +
25A VAL* 3.0 53.7 + - + +
49A LEU* 3.5 29.8 - - + -
50A GLU* 3.6 20.2 - - - -
53A ALA* 3.7 18.6 - - + -
54A ILE* 3.5 30.3 - - + -
90A TRP* 3.5 37.0 - + + +
94A LEU* 5.5 1.1 - - + -
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Residues in contact with SER 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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18A VAL 5.1 1.2 + - - -
19A GLN* 4.3 11.8 + - - -
20A HIS 3.3 0.4 - - - -
21A PHE* 1.4 78.2 - - - +
23A GLN* 1.3 57.3 + - - +
25A VAL* 3.5 6.1 + - - +
26A ARG* 3.0 45.5 + - - +
50A GLU* 6.1 0.2 - - - -
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Residues in contact with GLN 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 GLN 5.2 0.6 + - - +
20A HIS* 3.3 15.0 + - - +
22A SER* 1.3 73.7 - - - +
24A ILE* 1.4 61.3 + - + +
26A ARG* 3.5 25.1 - - - +
27A VAL* 3.0 41.9 + - + +
83A GLN* 3.1 25.9 + - - +
86A TRP* 3.2 26.3 - - + -
146A TYR* 4.0 11.8 + - - +
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Residues in contact with ILE 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 HIS 3.2 15.0 + - - +
21A PHE* 3.1 24.7 + - + +
23A GLN* 1.4 75.9 - - + +
25A VAL* 1.4 63.2 + - + +
27A VAL* 3.4 8.9 - - + +
28A LEU* 3.1 39.8 + - + +
49A LEU* 5.7 0.7 - - + -
86A TRP* 4.1 10.5 - - + -
87A THR* 4.1 27.6 - - + +
90A TRP* 3.8 38.1 - - + -
94A LEU* 5.0 5.6 - - + -
142A LEU* 4.0 21.8 - - + -
146A TYR* 5.6 2.5 - - + -
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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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21A PHE* 3.0 53.2 + - + +
22A SER* 3.9 6.1 - - - +
24A ILE* 1.4 71.3 - - + +
26A ARG* 1.4 54.8 + - - +
28A LEU* 3.1 2.3 + - - -
29A THR* 2.7 49.6 + - + +
46A LYS* 3.8 36.1 - - + +
49A LEU* 4.2 21.3 - - + -
50A GLU* 3.9 13.0 - - - +
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Residues in contact with ARG 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 SER* 3.0 39.4 + - - +
23A GLN* 3.5 33.3 - - - +
25A VAL* 1.4 75.6 - - - +
27A VAL* 1.4 64.8 + - + +
29A THR* 3.2 14.3 + - - -
30A GLU* 3.1 28.3 + - + +
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Residues in contact with VAL 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 GLN* 3.0 29.7 + - + +
24A ILE* 3.4 18.4 - - + +
26A ARG* 1.4 74.7 - - + +
28A LEU* 1.3 59.4 + - - +
30A GLU* 3.7 25.4 + - - +
141A ARG* 4.1 8.0 + - - -
142A LEU* 3.8 22.4 - - + -
145A LEU* 4.4 16.2 - - + +
146A TYR* 3.3 30.7 - - + +
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Residues in contact with LEU 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 ILE* 3.1 37.2 + - + +
25A VAL 3.1 5.8 + - - +
27A VAL* 1.3 76.2 - - - +
29A THR* 1.3 59.8 + - - +
30A GLU 3.6 1.1 + - - -
42A ILE* 4.9 4.0 - - - +
45A LEU* 3.8 7.8 - - + +
49A LEU* 4.1 23.1 - - + -
94A LEU* 4.4 1.3 - - + -
138A CYS* 3.8 30.7 - - + +
141A ARG* 3.0 66.3 + - + +
142A LEU* 3.9 23.8 - - + -
145A LEU* 5.0 2.2 - - + -
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Residues in contact with THR 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* 2.7 33.0 + - + +
26A ARG* 3.2 7.3 + - - -
28A LEU* 1.3 82.1 - - - +
30A GLU* 1.4 63.7 + - - +
42A ILE* 3.4 33.0 - - + +
45A LEU* 4.5 3.8 - - + -
46A LYS* 3.7 39.3 + - + +
49A LEU* 4.2 11.2 - - + -
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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