Contacts of the helix formed by residues 24 - 40 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B LEU 3.5 0.2 + - - -
21B ILE 3.0 16.3 + - - -
22B GLU 3.1 1.8 - - - -
23B THR* 1.3 77.9 - - - +
25B GLU* 1.3 63.4 + - - +
26B ARG 3.3 2.7 - - - -
27B GLU* 3.4 15.7 + - - +
28B ARG* 3.1 23.0 + - - +
1221D VAL* 6.4 0.4 - - - -
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 2.9 16.6 + - + +
23B THR* 3.1 18.6 + - - +
24B GLY* 1.3 76.0 - - - +
26B ARG* 1.3 60.6 + - - +
28B ARG* 2.8 43.2 + - - +
29B LEU* 2.9 55.8 + - + +
90B ARG* 5.1 3.6 - - - +
94B PHE* 3.6 33.2 - - + +
97B GLN* 5.5 4.1 + - - -
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174A GLU* 6.3 0.4 - - - +
1175A LEU* 3.3 39.2 - - + +
1178A ARG* 3.7 34.7 - - - +
1179A VAL* 5.4 2.8 - - - +
17B ASN* 4.0 16.8 + - - -
20B LEU* 2.9 33.6 + - + +
21B ILE* 3.7 27.4 - - - +
24B GLY 3.3 0.2 - - - -
25B GLU* 1.3 76.5 - - - +
27B GLU* 1.3 59.6 + - - +
29B LEU* 3.9 8.7 - - - +
30B LYS* 2.9 37.0 + - + +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE 5.8 0.4 + - - +
24B GLY* 3.4 15.8 + - - +
25B GLU 3.3 0.6 - - - -
26B ARG* 1.3 81.2 - - - +
28B ARG* 1.3 59.9 + - - +
30B LYS* 3.6 11.1 - - + +
31B GLU* 3.1 23.2 + - - +
1214D HIS* 5.9 6.5 - - + -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLY 3.1 13.8 + - - +
25B GLU* 2.8 45.0 + - - +
27B GLU* 1.3 75.6 - - - +
29B LEU* 1.3 68.5 + - - +
31B GLU* 3.3 9.4 + - - +
32B LEU* 3.1 43.2 + - + +
90B ARG* 4.0 17.8 - - - +
1218D LEU* 3.7 44.6 - - + +
1222D GLU* 6.2 0.2 - - - -
26F ARG* 4.5 6.6 - - - +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A LEU* 4.0 17.9 - - + -
20B LEU* 4.6 4.7 - - + -
25B GLU* 2.9 52.0 + - + +
26B ARG* 3.9 4.5 - - - +
28B ARG* 1.3 79.5 - - - +
30B LYS* 1.3 60.2 + - - +
32B LEU* 3.3 8.0 + - + +
33B LEU* 2.8 36.0 + - - +
87B LEU* 4.5 10.3 - - + -
90B ARG* 3.9 33.7 - - + +
91B ILE* 3.8 28.7 - - + +
94B PHE* 6.1 0.2 - - + -
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A LEU* 5.4 1.1 - - + +
1179A VAL* 3.9 32.7 - - + +
1182A GLU* 2.7 38.0 + - - -
26B ARG* 2.9 28.1 + - + +
27B GLU* 3.6 12.3 - - + +
29B LEU* 1.3 78.2 - - - +
31B GLU* 1.3 62.8 + - - +
33B LEU* 3.6 3.0 - - - +
34B ARG* 3.0 48.1 + - - +
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLU 3.1 11.9 + - - +
28B ARG* 3.5 8.8 - - - +
29B LEU 3.2 0.2 - - - -
30B LYS* 1.3 80.9 - - - +
32B LEU* 1.3 57.8 + - - +
34B ARG* 3.4 9.0 + - - +
35B ALA* 3.0 27.6 + - + +
1214D HIS* 3.3 29.2 + - - -
1218D LEU* 4.0 5.9 - - - +
17F ASN* 3.9 20.8 + - + +
21F ILE* 4.7 7.9 - - + -
26F ARG* 3.3 34.3 + - - +
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Residues in contact with LEU 32 (chain B).
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* 3.1 40.3 + - - +
29B LEU* 3.3 8.5 + - + +
31B GLU* 1.3 75.6 - - + +
33B LEU* 1.3 61.4 + - - +
35B ALA* 3.7 3.6 - - - +
36B LYS* 2.9 32.2 + - - +
90B ARG* 4.0 18.2 - - - +
21F ILE* 3.9 33.2 - - + +
26F ARG* 3.9 20.6 - - - +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A LEU* 4.4 7.2 - - + -
1176A MET* 3.6 33.9 - - + -
1179A VAL* 4.1 31.9 - - + -
29B LEU 2.8 22.8 + - - +
30B LYS 3.6 4.3 - - - +
32B LEU* 1.3 77.0 - - - +
34B ARG* 1.3 62.3 + - - +
36B LYS* 3.2 6.7 + - + +
37B LEU* 3.0 33.3 + - + +
83B VAL* 4.8 10.5 - - + +
87B LEU* 3.9 38.4 - - + -
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A VAL* 3.9 15.8 + - + +
1182A GLU* 4.4 8.7 + - - -
1183A PHE* 3.6 50.5 - - + +
1186A GLU* 3.2 31.8 + - - -
30B LYS* 3.0 42.4 + - - +
31B GLU* 3.7 7.6 - - - +
33B LEU* 1.3 76.4 - - - +
35B ALA* 1.3 57.7 + - - +
37B LEU* 3.4 3.4 + - - +
38B ILE* 3.0 38.6 + - + +
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLU* 3.0 17.9 + - + +
32B LEU 3.7 4.9 - - - +
33B LEU 3.2 0.2 - - - -
34B ARG* 1.3 77.7 - - - +
36B LYS* 1.3 57.5 + - + +
38B ILE* 3.5 0.6 + - - -
39B GLU* 3.0 25.8 + - - +
18F GLN* 3.2 33.1 + - - +
21F ILE* 3.8 35.7 - - + -
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 2.9 17.7 + - + +
33B LEU* 3.7 6.3 - - + +
35B ALA* 1.3 74.3 - - - +
37B LEU* 1.3 61.9 + - + +
39B GLU* 3.3 25.0 + - - +
40B CYS* 3.0 32.5 + - + +
83B VAL* 4.2 26.9 - - + +
86B GLU* 4.8 16.2 + - - +
21F ILE* 5.7 9.9 - - + +
22F GLU* 6.3 0.4 - - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176A MET* 5.2 10.8 - - - -
1179A VAL* 5.2 5.8 - - + -
1180A MET* 5.1 9.6 - - - -
1183A PHE* 4.3 12.8 - - + -
33B LEU* 3.0 26.2 + - + +
34B ARG* 3.7 5.4 - - - +
36B LYS* 1.3 76.9 - - + +
38B ILE* 1.3 59.5 + - - +
40B CYS* 3.5 4.8 - - - -
42B TRP* 3.0 84.6 + - + +
43B LYS* 3.5 3.0 + - - -
79B VAL* 4.4 11.7 - - + -
80B PRO* 4.2 20.4 - - + -
83B VAL* 5.0 8.1 - - + -
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183A PHE* 3.8 25.6 - - + -
34B ARG* 3.0 24.6 + - + +
35B ALA 3.7 4.3 - - - +
37B LEU* 1.3 77.2 - - - +
39B GLU* 1.3 64.7 + - - +
41B GLY* 3.3 13.0 + - - -
43B LYS* 4.2 24.3 - - + +
44B ASP* 5.2 3.3 - - - +
18F GLN* 3.6 33.9 - - + +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA 3.0 17.7 + - - +
36B LYS* 3.3 37.5 + - - +
38B ILE* 1.3 79.1 - - - +
40B CYS* 1.3 59.5 + - - +
41B GLY* 3.2 1.6 + - - -
18F GLN* 4.2 4.5 - - - +
21F ILE* 5.7 2.3 - - - +
22F GLU* 3.6 46.5 - - - +
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Residues in contact with CYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 3.0 20.7 + - + +
37B LEU* 3.5 14.1 - - - -
38B ILE 3.3 0.4 - - - -
39B GLU* 1.3 77.1 - - + +
41B GLY* 1.3 58.0 + - - +
42B TRP* 3.6 17.2 + - - -
45B GLN* 5.9 0.3 + - - -
80B PRO* 4.0 26.5 - - + -
83B VAL* 5.7 1.3 - - - -
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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