Contacts of the helix formed by residues 23 - 41 (chain A) in PDB entry 3EDH
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 THR 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN 5.7 0.2 - - - +
22A PHE* 1.3 77.7 - - - +
24A GLY* 1.3 66.1 + - - +
25A SER* 3.5 8.3 + - - -
26A GLN* 2.9 41.5 + - - +
27A ARG* 3.0 23.8 + - - +
82A LYS* 5.0 10.5 - - - +
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Residues in contact with GLY 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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23A THR* 1.3 73.0 - - - +
25A SER* 1.3 56.0 + - - +
27A ARG* 3.4 26.4 + - - +
28A ALA* 3.0 28.8 + - - +
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 3.2 8.3 + - - -
24A GLY* 1.3 74.7 - - - +
26A GLN* 1.3 65.4 + - - +
28A ALA* 3.2 8.3 + - - +
29A VAL* 3.0 30.5 + - - +
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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
----------------------------------------------------------
21A ASN 4.4 2.4 + - - -
22A PHE* 3.3 32.4 - - + +
23A THR* 2.9 46.8 + - - +
25A SER* 1.3 76.1 - - - +
27A ARG* 1.3 63.9 + - - +
29A VAL* 3.1 10.5 + - - +
30A PHE* 3.1 32.7 + - + -
59A TYR* 5.8 2.6 - - - -
81A GLY* 4.9 1.2 - - - -
82A LYS* 3.4 25.9 + - - +
85A ASP* 2.8 36.9 - - + +
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Residues in contact with ARG 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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19A ILE* 3.7 36.2 - - + +
20A GLY 4.9 3.4 - - - -
22A PHE* 2.8 41.6 + - + +
23A THR 3.0 10.7 + - - +
24A GLY* 3.6 25.8 - - - +
26A GLN* 1.3 75.1 - - - +
28A ALA* 1.3 63.4 + - - +
30A PHE* 3.1 20.2 + - - +
31A ARG* 3.1 22.2 + - - +
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Residues in contact with ALA 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 GLY 3.0 17.0 + - - +
25A SER* 3.5 8.5 - - - +
26A GLN 3.2 0.2 - - - -
27A ARG* 1.3 77.6 - - - +
29A VAL* 1.3 56.7 + - + +
31A ARG* 3.3 10.7 + - - +
32A GLN* 2.9 28.7 + - - +
35A ARG* 4.9 2.4 + - - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 3.0 25.7 + - - +
26A GLN* 3.1 9.8 + - - +
28A ALA* 1.3 73.8 - - + +
30A PHE* 1.3 68.3 + - + +
32A GLN* 3.2 16.0 + - - +
33A ALA* 2.9 22.3 + - - +
85A ASP 3.5 24.7 - - - +
86A LYS* 4.0 0.9 - - - -
87A PHE* 3.5 29.2 - - + +
90A VAL* 4.5 6.1 - - + -
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Residues in contact with PHE 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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19A ILE* 3.9 14.1 - - + -
22A PHE* 3.7 52.5 - + - -
26A GLN* 3.1 25.3 + - + -
27A ARG* 3.1 12.1 + - - +
29A VAL* 1.3 76.7 - - + +
31A ARG* 1.3 62.7 + - - +
33A ALA* 3.3 3.1 + - - +
34A MET* 3.0 33.6 + - + +
57A PHE* 3.7 38.2 - + + -
79A ILE* 3.6 29.8 - - + -
85A ASP* 4.8 4.7 - - + -
90A VAL* 4.1 22.9 - - + -
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Residues in contact with ARG 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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17A PHE* 3.6 6.3 - - - -
19A ILE* 4.0 23.6 - - + +
27A ARG* 3.1 15.6 + - - +
28A ALA* 3.7 9.4 - - - +
30A PHE* 1.3 76.3 - - - +
32A GLN* 1.3 56.9 + - - +
34A MET* 3.3 11.7 + - + +
35A ARG* 2.8 46.7 + - - +
47A GLU* 2.6 41.6 + - - -
216A DMS 2.9 38.1 + - - +
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Residues in contact with GLN 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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28A ALA 2.9 16.2 + - - +
29A VAL* 3.2 19.5 + - - +
31A ARG* 1.3 75.6 - - - +
33A ALA* 1.3 58.1 + - - +
35A ARG* 3.3 27.1 + - - +
36A HIS* 3.0 22.7 + - - +
87A PHE* 3.6 36.8 - - + +
213A DMS 5.2 9.0 + - - -
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Residues in contact with ALA 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 VAL 2.9 16.5 + - - +
30A PHE 3.6 1.1 - - - +
32A GLN* 1.3 74.7 - - - +
34A MET* 1.3 64.4 + - - +
36A HIS* 3.2 11.4 + - - +
37A TRP* 3.3 19.8 + - - -
87A PHE* 3.7 14.5 - - + +
90A VAL* 3.5 32.5 - - + -
91A VAL* 3.8 17.2 - - + +
94A LEU* 3.8 6.3 - - + -
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Residues in contact with MET 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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17A PHE* 3.7 32.3 - - + -
19A ILE* 4.8 1.1 - - + -
30A PHE* 3.0 25.5 + - + +
31A ARG* 3.7 13.2 - - + +
33A ALA* 1.3 75.7 - - - +
35A ARG* 1.3 62.6 + - - +
37A TRP* 3.2 5.4 + - - +
38A GLU* 3.0 24.6 + - - +
45A PHE* 3.5 49.0 - - + -
57A PHE* 3.7 27.8 - - + -
94A LEU* 3.8 16.6 - - + -
216A DMS 3.7 18.2 - - + +
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Residues in contact with ARG 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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28A ALA 4.9 2.0 + - - -
31A ARG* 2.8 39.8 + - - +
32A GLN* 3.6 29.7 - - - +
34A MET* 1.3 76.5 - - - +
36A HIS* 1.3 57.4 + - - +
38A GLU* 3.1 12.8 + - - +
39A LYS* 2.9 36.3 + - - +
213A DMS 2.8 47.8 + - - +
216A DMS 3.7 16.5 + - + +
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Residues in contact with HIS 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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32A GLN 3.0 13.6 + - - +
33A ALA 3.4 9.6 - - - +
34A MET 3.2 0.4 - - - -
35A ARG* 1.3 77.8 - - - +
37A TRP* 1.3 63.5 + - - +
39A LYS* 3.4 17.3 + - + +
40A HIS* 3.2 49.0 + + - +
87A PHE* 3.6 22.9 - + + -
91A VAL* 3.9 11.4 - - + +
181A ARG* 3.7 18.0 - - - +
182A LEU* 3.0 57.8 + - + +
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Residues in contact with TRP 37 (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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33A ALA 3.3 16.4 + - - -
34A MET 3.2 8.4 + - - +
36A HIS* 1.3 80.5 - - - +
38A GLU* 1.3 61.5 + - - +
40A HIS 3.4 0.2 + - - -
41A THR* 2.8 51.0 + - + +
43A VAL* 4.7 4.0 - - + -
45A PHE* 3.8 16.4 - + + -
91A VAL* 3.1 32.3 + - + +
94A LEU* 3.5 21.8 - - + +
95A GLY* 3.4 29.8 - - - -
98A VAL* 4.0 26.5 - - + -
100A PHE* 4.2 11.9 - + - -
146A ILE* 5.1 1.6 - - + -
182A LEU* 3.5 33.0 - - + -
186A ASP* 5.2 4.7 - - + -
190A ALA* 3.8 24.7 - - + -
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Residues in contact with GLU 38 (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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34A MET 3.0 14.9 + - - +
35A ARG* 3.1 13.2 + - - +
37A TRP* 1.3 77.6 - - - +
39A LYS* 1.3 59.2 + - - +
41A THR 2.9 17.7 - - - +
43A VAL 3.5 23.2 - - - +
44A THR* 3.6 9.3 - - + -
45A PHE* 2.8 39.6 + - + +
216A DMS 3.4 28.4 - - - +
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Residues in contact with LYS 39 (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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35A ARG* 2.9 23.8 + - - +
36A HIS* 3.5 20.1 - - + +
38A GLU* 1.3 77.8 - - - +
40A HIS* 1.3 75.3 + - + +
191A ARG* 5.4 0.3 + - - -
212A DMS 3.6 44.8 + - + +
213A DMS 2.8 51.6 + - - +
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Residues in contact with HIS 40 (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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36A HIS* 3.2 48.3 + + - +
37A TRP 3.4 3.1 + - - +
38A GLU 3.2 0.2 - - - -
39A LYS* 1.3 93.7 - - + +
41A THR* 1.3 62.2 + - + +
182A LEU* 4.5 2.6 - - + +
187A ILE* 3.4 39.7 - - + +
191A ARG* 2.9 39.9 + - - +
212A DMS 3.5 18.8 + - - -
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Residues in contact with THR 41 (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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37A TRP* 2.8 31.6 + - + +
38A GLU 2.9 18.5 - - - +
39A LYS 4.7 0.2 - - - -
40A HIS* 1.3 88.2 - - + +
42A CYS* 1.3 61.1 + - - +
43A VAL* 3.2 27.9 + - - +
182A LEU* 5.1 0.2 - - + -
187A ILE* 4.5 13.2 - - + +
190A ALA* 4.0 26.7 - - + -
191A ARG* 4.4 11.0 - - + +
198A CYS* 4.8 2.2 - - - -
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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
------------------------------------------------------------
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