Contacts of the helix formed by residues 24 - 40 (chain F) in PDB entry 4DHX
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 GLY 24 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F LEU 3.5 0.4 + - - -
21F ILE 3.1 15.4 + - - -
22F GLU 3.3 0.8 - - - -
23F THR* 1.3 77.5 + - - +
25F GLU* 1.3 64.6 + - - +
26F ARG 3.1 2.9 - - - -
27F GLU* 3.1 21.8 + - - +
28F ARG* 3.1 24.4 + - - +
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Residues in contact with GLU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU* 3.2 20.7 + - + +
23F THR* 3.2 16.3 - - - +
24F GLY* 1.3 78.6 - - - +
26F ARG* 1.3 55.3 + - - +
28F ARG* 2.9 40.4 + - - +
29F LEU* 2.8 58.1 + - + +
90F ARG* 4.9 11.1 + - - +
91F ILE* 6.2 0.4 - - - -
94F PHE* 3.6 36.4 - - + +
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Residues in contact with ARG 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 4.5 5.3 - - - +
31B GLU* 3.3 30.1 + - - -
32B LEU* 3.9 21.7 - - - +
1214D HIS* 4.6 2.6 + - - -
1215D LEU* 4.6 18.5 - - + +
1218D LEU* 3.5 34.0 - - - +
1219D PHE* 3.4 24.4 - - + -
17F ASN* 4.5 9.6 + - - -
20F LEU* 2.8 28.7 + - + +
21F ILE* 3.8 31.0 - - + +
24F GLY 3.1 0.2 - - - -
25F GLU* 1.3 77.5 - - - +
27F GLU* 1.3 67.9 + - - +
29F LEU* 3.3 12.0 + - - +
30F LYS 3.1 18.0 + - - -
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Residues in contact with GLU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219D PHE* 5.7 1.2 - - - -
24F GLY* 3.1 14.7 + - - +
26F ARG* 1.3 86.7 + - - +
28F ARG* 1.3 62.0 + - + +
30F LYS* 3.1 38.2 + - - +
31F GLU* 3.2 20.6 + - - +
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Residues in contact with ARG 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F THR* 3.4 21.8 + - - -
24F GLY* 3.1 10.3 + - - +
25F GLU* 2.9 55.2 + - - +
27F GLU* 1.3 76.8 - - + +
29F LEU* 1.3 63.9 + - - +
31F GLU* 3.3 15.8 + - - +
32F LEU* 3.1 23.4 + - - +
94F PHE* 4.4 7.7 - - - -
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Residues in contact with LEU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215D LEU* 3.9 20.0 - - + -
1219D PHE* 4.2 9.4 - - + -
20F LEU* 4.4 4.5 - - + -
25F GLU* 2.8 47.5 + - + +
26F ARG* 3.3 8.3 + - - +
28F ARG* 1.3 74.0 - - - +
30F LYS* 1.3 60.4 + - - +
32F LEU* 3.4 5.5 + - + +
33F LEU* 2.9 30.5 + - - +
87F LEU* 4.5 19.3 - - + +
90F ARG* 4.2 30.7 - - + +
91F ILE* 3.7 28.9 - - + +
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Residues in contact with LYS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219D PHE* 3.6 36.6 - - + +
1222D GLU* 2.9 42.9 + - - +
1223D GLU* 5.2 2.9 - - - +
26F ARG 3.1 7.8 + - - +
27F GLU* 3.1 39.9 + - - +
28F ARG 3.2 0.2 - - - -
29F LEU* 1.3 77.2 - - - +
31F GLU* 1.3 65.6 + - - +
33F LEU* 3.2 2.6 + - - +
34F ARG* 3.0 24.8 + - + +
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F GLU 3.2 9.3 + - - +
28F ARG* 3.3 17.9 + - - +
30F LYS* 1.3 82.5 - - + +
32F LEU* 1.3 62.4 + - - +
34F ARG* 3.5 6.6 + - - +
35F ALA* 3.2 22.6 + - + +
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Residues in contact with LEU 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ARG 3.1 16.3 + - - +
29F LEU* 3.8 6.1 - - + +
31F GLU* 1.3 74.3 - - - +
33F LEU* 1.3 66.9 + - - +
35F ALA* 3.4 9.6 + - + +
36F LYS* 3.1 46.6 + - + +
87F LEU* 4.7 6.5 - - + -
90F ARG* 3.3 46.4 - - - +
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Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1216D VAL* 4.1 25.8 - - + +
1219D PHE* 3.7 37.7 - - + -
1220D LEU* 5.2 2.2 - - + +
1223D GLU* 6.5 1.3 - - + -
29F LEU 2.9 18.7 + - - +
30F LYS* 3.6 4.9 - - - +
32F LEU* 1.3 78.3 - - - +
34F ARG* 1.3 63.5 + - - +
36F LYS* 3.2 4.1 + - - +
37F LEU* 3.0 42.3 + - + +
79F VAL* 5.5 2.7 - - + -
83F VAL* 3.7 26.7 - - + -
84F LYS* 6.6 0.2 - - + -
87F LEU* 4.0 23.3 - - + +
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Residues in contact with ARG 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222D GLU* 5.4 1.4 - - - +
1223D GLU* 2.9 46.6 + - + +
1226D GLN* 5.0 13.3 - - - +
1230D GLU* 4.8 6.5 + - - -
30F LYS* 3.0 18.1 + - + +
31F GLU* 3.7 7.4 - - - +
33F LEU* 1.3 78.0 - - - +
35F ALA* 1.3 63.0 + - - +
37F LEU* 3.2 7.3 + - - +
38F ILE* 2.9 44.7 + - + +
43F LYS* 3.9 19.4 - - - +
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Residues in contact with ALA 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F GLU* 3.2 11.7 + - + +
32F LEU* 3.6 16.8 - - + +
34F ARG* 1.3 78.7 - - - +
36F LYS* 1.3 59.1 + - + +
38F ILE* 4.0 5.3 - - - +
39F GLU* 3.0 32.4 + - - +
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Residues in contact with LYS 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LEU* 3.1 47.1 + - + +
33F LEU 3.2 4.7 + - - +
35F ALA* 1.3 77.8 - - + +
37F LEU* 1.3 62.2 + - - +
39F GLU* 3.9 14.8 + - - +
40F CYS* 3.2 28.2 + - - +
83F VAL* 4.0 35.0 - - + +
86F GLU* 2.6 35.2 + - - +
87F LEU* 4.9 7.4 - - + -
90F ARG* 6.0 1.3 - - - +
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Residues in contact with LEU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220D LEU* 3.8 26.5 - - + -
1223D GLU* 5.2 8.3 - - + -
33F LEU* 3.0 40.6 + - + +
34F ARG* 3.2 6.9 + - - +
36F LYS* 1.3 75.9 - - - +
38F ILE* 1.3 64.7 + - + +
40F CYS* 3.3 5.4 - - - -
42F TRP* 2.8 74.8 + - + +
43F LYS 4.4 0.9 - - - -
79F VAL* 4.2 20.2 - - + -
80F PRO* 4.3 9.6 - - + -
83F VAL* 4.5 4.7 - - + -
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Residues in contact with ILE 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223D GLU* 5.3 2.9 - - + +
34F ARG* 2.9 53.9 + - + +
35F ALA* 4.0 4.7 - - - +
37F LEU* 1.3 78.7 - - + +
39F GLU* 1.3 67.4 + - - +
41F GLY* 3.0 14.6 + - - -
42F TRP* 5.6 2.0 - - + -
43F LYS* 4.0 37.9 - - + +
44F ASP* 4.6 7.5 - - - +
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Residues in contact with GLU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ALA 3.0 20.6 + - - +
36F LYS* 3.9 16.2 + - - +
38F ILE* 1.3 81.2 - - - +
40F CYS* 1.3 71.9 + - - +
41F GLY* 3.4 0.9 + - - -
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Residues in contact with CYS 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LYS 3.2 22.0 + - - +
37F LEU* 3.3 13.9 - - - -
38F ILE 3.2 0.2 - - - -
39F GLU* 1.3 90.6 - - - +
41F GLY* 1.3 56.7 + - - +
42F TRP* 3.8 13.9 - - - -
45F GLN* 4.3 8.0 + - - -
80F PRO* 3.9 28.3 - - + -
83F VAL* 4.9 5.2 - - + -
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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