Contacts of the helix formed by residues 24 - 36 (chain A) in PDB entry 4IQJ
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 LYS 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLN* 4.1 8.5 - - - +
22A ALA 3.7 1.9 + - - +
23A ALA* 1.3 72.6 - - - +
25A LEU* 1.3 60.6 + - - +
26A GLN* 3.4 4.9 - - + +
27A ASP* 3.0 38.3 + - - +
28A LEU* 3.1 19.9 - - - +
216A VAL* 4.7 0.2 - - - +
563A MET 2.8 25.4 + - - -
564A ARG* 3.3 25.1 - - - +
566A GLU* 3.6 7.6 + - - +
567A GLY* 3.4 32.3 - - - +
568A LEU* 3.4 20.6 - - + +
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Residues in contact with LEU 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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14A THR* 3.8 22.0 - - + -
15A GLN* 3.3 17.6 + - - +
16A PHE* 4.0 20.2 - - + -
23A ALA 3.9 0.4 + - - -
24A LYS* 1.3 74.3 - - - +
26A GLN* 1.3 62.4 + - - +
28A LEU* 4.3 4.2 - - + +
29A LEU* 3.3 32.9 + - + +
44A MET* 5.3 0.2 - - - -
55A GLU* 3.5 46.2 - - + +
56A PHE* 3.6 41.3 - - + +
59A LYS* 4.0 14.8 - - + +
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Residues in contact with GLN 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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24A LYS* 3.4 4.1 - - + +
25A LEU* 1.3 76.4 - - - +
27A ASP* 1.3 68.0 + - + +
28A LEU 3.1 2.7 + - - -
29A LEU* 3.2 13.5 + - - +
30A LYS* 3.4 20.4 + - + +
59A LYS* 4.4 27.1 + - - +
63A MET* 3.7 31.8 - - - +
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Residues in contact with ASP 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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24A LYS* 3.0 38.0 + - - +
26A GLN* 1.3 78.6 - - + +
28A LEU* 1.3 78.7 + - - +
30A LYS* 3.3 41.6 - - - +
31A TRP* 3.3 11.4 + - - +
216A VAL* 3.5 18.6 - - + +
564A ARG* 3.7 25.3 + - - +
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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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12A GLN* 4.0 23.8 - - + +
14A THR* 3.9 28.5 - - + -
23A ALA* 4.2 6.5 - - + -
24A LYS 3.1 18.2 - - - +
25A LEU* 4.3 4.3 - - + +
26A GLN 3.1 1.2 - - - -
27A ASP* 1.3 83.1 + - - +
29A LEU* 1.3 62.7 + - + +
31A TRP* 3.3 3.5 + - + +
32A VAL* 3.2 28.4 + - + +
42A LEU* 3.9 19.3 - - + -
56A PHE* 5.5 2.0 - - + -
216A VAL* 3.9 19.5 - - + -
251A VAL* 3.4 34.5 - - + -
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Residues in contact with LEU 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 LEU* 3.3 20.0 - - + +
26A GLN* 3.2 5.0 + - - +
28A LEU* 1.3 78.6 - - + +
30A LYS* 1.3 56.9 + - - +
32A VAL* 3.5 5.9 + - - +
33A LYS* 2.9 27.5 + - - +
42A LEU* 3.6 23.3 - - + -
56A PHE* 3.9 16.6 - - + +
59A LYS* 3.7 16.4 - - + +
60A ALA* 3.6 46.2 - - + +
63A MET* 3.7 20.8 - - + +
65A VAL* 4.1 17.2 - - + +
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Residues in contact with LYS 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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26A GLN* 3.4 15.3 + - + +
27A ASP* 3.3 35.1 - - - +
29A LEU* 1.3 76.3 - - - +
31A TRP* 1.3 63.9 + - + +
33A LYS* 3.6 2.6 - - - +
34A GLU* 2.8 51.6 + - + +
63A MET* 3.7 24.8 - - + -
536A GLN* 5.8 3.8 - - - +
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Residues in contact with TRP 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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27A ASP 3.6 9.6 - - - +
28A LEU 3.3 9.5 + - - +
29A LEU 3.3 0.4 - - - -
30A LYS* 1.3 81.4 - - + +
32A VAL* 1.3 57.9 + - - +
34A GLU* 4.2 15.3 - - + -
35A THR* 2.7 52.5 + - - -
216A VAL* 3.8 20.3 + - + -
217A ARG* 3.7 43.7 - - + +
250A TYR* 6.5 0.9 - + - -
251A VAL* 3.2 45.9 + - + -
253A THR* 4.8 11.5 + - - -
256A GLU* 6.1 0.4 - - - -
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Residues in contact with VAL 32 (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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9A HIS* 5.9 1.6 - - + -
28A LEU* 3.2 15.1 + - + +
29A LEU* 3.7 8.5 - - - +
31A TRP* 1.3 77.2 - - - +
33A LYS* 1.3 61.3 + - - +
35A THR* 4.3 3.7 - - - -
36A THR* 3.2 27.0 + - - +
40A PRO* 4.2 15.4 - - + +
41A ALA 4.0 20.0 - - - +
42A LEU* 3.7 29.2 - - + -
65A VAL* 4.5 9.9 - - + -
251A VAL* 4.2 20.2 - - + -
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Residues in contact with LYS 33 (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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29A LEU 2.9 18.0 + - - +
30A LYS* 3.6 9.4 - - - +
31A TRP 3.2 0.2 - - - -
32A VAL* 1.3 77.6 - - - +
34A GLU* 1.3 64.8 + - + +
36A THR 3.2 21.4 - - - +
37A PRO* 3.6 18.1 + - - +
40A PRO* 3.9 29.7 - - + +
63A MET* 3.6 33.7 + - + +
64A GLY* 3.9 10.3 + - - -
65A VAL* 4.0 8.3 - - + -
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Residues in contact with GLU 34 (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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30A LYS* 2.8 45.5 + - + +
31A TRP* 4.2 19.2 + - + +
33A LYS* 1.3 76.4 - - + +
35A THR* 1.3 60.8 + - - +
37A PRO* 4.4 8.1 - - - +
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Residues in contact with THR 35 (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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31A TRP* 2.7 46.5 + - - +
32A VAL* 4.3 4.0 - - - -
34A GLU* 1.3 80.1 - - - +
36A THR* 1.3 67.0 + - - +
37A PRO* 3.6 6.7 - - - +
251A VAL* 6.5 0.7 - - - -
252A LYS 5.6 0.2 - - - +
253A THR* 3.7 36.1 + - + +
254A PRO* 4.1 9.4 - - + -
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Residues in contact with THR 36 (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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6A LYS* 4.5 21.5 - - + +
7A PHE 4.0 16.9 + - - +
32A VAL* 3.2 11.9 + - - +
33A LYS 3.2 9.3 - - - +
35A THR* 1.3 90.0 + - - +
37A PRO* 1.3 61.7 - - + +
38A GLU* 3.6 22.7 - - + +
39A ASP 5.2 0.4 - - - +
40A PRO* 3.4 26.4 - - + +
254A PRO* 4.7 9.2 - - - +
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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