Contacts of the helix formed by residues 13 - 34 (chain T) in PDB entry 5KHU
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 LEU 13 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12T THR* 3.8 29.2 - - - +
14T ARG* 3.8 27.4 - - - +
16T SER* 4.6 14.4 - - - +
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Residues in contact with ARG 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T LEU* 3.8 25.6 - - - +
15T GLY* 3.8 28.7 - - - +
17T ALA* 4.3 17.3 - - - +
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Residues in contact with GLY 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ARG* 3.8 25.1 - - - +
16T SER* 3.8 28.9 - - - +
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Residues in contact with SER 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T LEU* 4.6 14.4 - - - +
15T GLY* 3.8 29.6 - - - +
17T ALA* 3.8 25.1 - - - +
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Residues in contact with ALA 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ARG* 4.3 17.0 - - - +
16T SER* 3.8 27.4 - - - +
18T GLU* 3.8 28.3 - - - +
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Residues in contact with GLU 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17T ALA* 3.8 28.7 - - - +
19T ILE* 3.8 27.4 - - - +
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Residues in contact with ILE 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T GLU* 3.8 25.6 - - - +
20T VAL* 3.8 28.9 - - - +
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Residues in contact with VAL 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T ILE* 3.8 28.3 - - - +
21T ALA* 3.8 26.7 - - - +
23T PHE* 4.6 15.9 - - - +
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Residues in contact with ALA 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T VAL* 3.8 25.1 - - - +
22T GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T ALA* 3.8 28.9 - - - +
23T PHE* 3.8 26.5 - - - +
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Residues in contact with PHE 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T VAL* 4.6 16.6 - - - +
22T GLU* 3.8 29.4 - - - +
24T PHE* 3.8 26.5 - - - +
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Residues in contact with PHE 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23T PHE* 3.8 24.7 - - - +
25T SER* 3.8 28.7 - - - +
27T GLY* 4.5 19.1 - - - +
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Residues in contact with SER 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T PHE* 3.8 24.7 - - - +
26T PHE* 3.8 29.4 - - - +
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Residues in contact with PHE 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25T SER* 3.8 29.8 - - - +
27T GLY* 3.8 26.0 - - - +
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Residues in contact with GLY 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T PHE* 4.5 15.9 - - - +
26T PHE* 3.8 28.5 - - - +
28T ILE* 3.8 26.0 - - - +
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Residues in contact with ILE 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T GLY* 3.8 29.8 - - - +
29T ASN* 3.8 26.7 - - - +
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Residues in contact with ASN 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28T ILE* 3.8 25.1 - - - +
30T SER* 3.8 29.4 - - - +
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Residues in contact with SER 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T ASN* 3.8 29.4 - - - +
31T ILE* 3.8 26.9 - - - +
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Residues in contact with ILE 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T SER* 3.8 26.7 - - - +
32T LEU* 3.8 29.4 - - - +
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Residues in contact with LEU 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31T ILE* 3.8 29.2 - - - +
33T TYR* 3.8 26.0 - - - +
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Residues in contact with TYR 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T LEU* 3.8 29.2 - - - +
34T GLN* 3.8 26.9 - - - +
36T GLY* 4.5 13.9 - - - +
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Residues in contact with GLN 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T TYR* 3.8 29.2 - - - +
35T ARG* 3.8 26.5 - - - +
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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