Contacts of the helix formed by residues 24 - 39 (chain C) in PDB entry 1EFU
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C THR* 4.1 9.5 - - - +
17C ILE 3.8 4.3 - - - -
18C GLY* 3.4 39.5 + - - +
19C HIS 4.5 12.3 + - - +
20C VAL* 5.3 8.3 + - - +
22C HIS 5.4 0.4 - - - -
23C GLY* 1.3 75.7 - - - +
25C THR* 1.3 62.5 + - - +
26C THR 3.2 0.2 - - - -
27C LEU* 3.6 1.7 + - - +
28C THR* 2.9 34.2 + - - -
80C ASP* 3.1 42.3 + - - +
81C CYS 3.9 17.4 + - - -
82C PRO* 4.1 8.7 - - - +
104C VAL* 3.9 28.5 - - + -
271D PHE* 4.9 0.7 - - - -
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Residues in contact with THR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS* 1.3 76.5 - - - +
26C THR* 1.3 61.8 + - - +
28C THR* 3.5 2.8 + - - -
29C ALA* 3.1 24.9 + - - +
80C ASP* 4.9 2.6 + - - -
271D PHE* 3.3 19.0 - - - -
274D GLU* 3.0 44.8 + - + +
275D VAL* 3.6 24.0 - - + +
278D MET* 3.7 14.6 - - + -
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Residues in contact with THR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLY* 4.1 16.3 - - - -
24C LYS 3.2 0.6 - - - -
25C THR* 1.3 75.2 - - - +
27C LEU* 1.3 60.1 + - - +
29C ALA* 3.0 5.9 + - - +
30C ALA* 2.9 26.2 + - - +
135C ASN* 5.3 0.4 - - - -
174C ALA* 3.5 19.5 - - + -
175C LEU* 4.0 22.6 - - + +
178C LEU* 3.9 20.3 - - + +
278D MET* 3.5 24.3 - - - -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR* 4.8 4.7 - - + -
23C GLY 3.2 17.4 + - - +
24C LYS 3.9 2.5 - - - +
26C THR* 1.3 77.1 - - - +
28C THR* 1.3 58.1 + - - +
30C ALA* 3.0 4.8 + - - +
31C ILE* 2.8 40.1 + - + +
102C ILE* 4.3 5.2 - - + -
104C VAL* 3.7 23.8 - - + -
133C PHE* 3.4 54.7 - - + -
174C ALA* 3.6 14.1 - - + +
188C ILE* 3.8 12.8 - - + -
191C LEU* 3.7 22.9 - - + -
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Residues in contact with THR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR* 4.0 2.9 - - - +
24C LYS 2.9 21.8 + - - -
25C THR 3.7 4.9 - - - -
26C THR 3.2 0.2 - - - -
27C LEU* 1.3 76.9 - - - +
29C ALA* 1.3 60.8 + - - +
31C ILE* 3.4 11.8 + - - +
32C THR* 3.3 22.5 + - - +
67C VAL* 4.3 10.3 - - + -
69C TYR* 4.9 2.0 - - + -
78C HIS* 3.0 43.8 + - + +
271D PHE* 3.7 13.1 - - + -
275D VAL* 3.7 21.5 - - + -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR 3.1 7.5 + - - +
26C THR 3.0 7.9 + - - +
28C THR* 1.3 77.8 - - - +
30C ALA* 1.3 62.4 + - - +
32C THR* 2.7 21.1 + - - -
33C THR* 3.0 12.5 + - - -
178C LEU* 3.9 5.6 - - + -
275D VAL* 3.6 18.2 - - - +
278D MET* 3.1 38.6 - - + +
279D SER* 3.7 8.5 - - - +
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Residues in contact with ALA 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C THR 2.9 11.3 + - - +
27C LEU* 3.3 11.9 - - - +
29C ALA* 1.3 77.6 - - - +
31C ILE* 1.3 54.9 + - - +
33C THR* 4.6 0.4 - - - -
34C VAL* 3.0 37.5 + - + +
174C ALA* 3.9 19.5 - - - +
177C ALA* 4.3 4.5 - - + -
178C LEU* 3.5 15.1 - - + +
188C ILE* 3.7 24.9 - - + +
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Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 2.8 33.0 + - + +
28C THR* 3.5 16.6 - - - +
29C ALA 3.1 0.4 - - - -
30C ALA* 1.3 77.6 - - - +
32C THR* 1.3 58.4 + - - +
34C VAL* 4.3 0.2 - - - +
35C LEU* 3.0 47.8 + - + +
69C TYR* 3.6 46.7 - - + +
78C HIS* 4.2 10.1 - - + -
102C ILE* 4.4 6.1 - - + -
188C ILE* 3.8 13.9 - - + -
191C LEU* 4.1 20.9 - - + -
192C ALA* 5.7 2.2 - - + -
195C LEU* 5.3 4.5 - - + -
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C THR 3.3 10.9 + - - +
29C ALA* 2.7 20.6 + - - -
31C ILE* 1.3 73.6 - - - +
33C THR* 1.3 66.8 + - - -
35C LEU* 3.8 0.7 - - - +
36C ALA* 2.8 28.9 + - - +
67C VAL* 3.7 28.3 - - + -
68C GLU 4.0 7.9 - - - +
69C TYR* 3.8 22.2 - - + -
275D VAL* 4.6 2.6 - - + +
279D SER* 3.3 16.3 + - - -
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Residues in contact with THR 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ALA 3.0 14.6 + - - -
30C ALA 4.2 1.1 - - - -
32C THR* 1.3 81.5 + - - +
34C VAL* 1.3 64.0 + - + +
36C ALA* 3.6 5.1 - - - +
37C LYS* 3.1 33.6 + - - +
177C ALA 5.9 0.9 - - - +
178C LEU* 3.8 12.8 - - + +
279D SER* 3.8 25.7 + - - +
281D GLN 3.6 6.3 - - - +
282D SER* 3.3 34.5 - - - +
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA* 3.0 24.2 + - - +
33C THR* 1.3 76.8 - - + +
35C LEU* 1.3 64.1 + - - +
37C LYS* 3.5 7.3 - - + +
38C THR* 2.7 36.4 + - - +
177C ALA* 4.5 9.4 - - + +
178C LEU* 6.0 0.4 - - - -
185C GLU* 3.8 46.7 - - + +
188C ILE* 4.1 13.5 - - + -
189C LEU* 3.6 31.0 - - + -
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE* 3.0 32.9 + - + +
32C THR* 4.0 2.5 - - - +
34C VAL* 1.3 77.2 - - + +
36C ALA* 1.3 57.0 + - - +
39C TYR* 3.0 49.9 + - + +
40C GLY 4.0 0.3 + - - -
69C TYR* 3.4 38.1 - - + -
70C ASP 3.7 17.9 - - - +
71C THR* 4.1 12.6 - - + -
188C ILE* 5.6 1.6 - - + -
189C LEU* 3.4 26.5 - - + -
192C ALA* 3.8 19.7 - - + -
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C THR 2.8 19.8 + - - +
33C THR* 3.6 5.6 - - - +
35C LEU* 1.3 76.8 - - - +
37C LYS* 1.3 57.4 + - - +
40C GLY 2.7 31.5 + - - +
41C GLY* 2.8 34.8 + - - +
42C ALA 3.7 0.7 - - - -
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C THR* 3.1 29.2 + - - +
34C VAL* 3.5 10.8 - - - +
36C ALA* 1.3 79.2 - - - +
38C THR* 1.3 69.1 + - - +
40C GLY 4.8 1.0 + - - -
42C ALA 3.8 11.8 - - - +
180C GLY* 4.6 0.6 - - - -
185C GLU* 3.1 28.7 + - - +
282D SER* 2.7 35.5 + - - -
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Residues in contact with THR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 2.7 28.4 + - - +
37C LYS* 1.3 84.9 - - - +
39C TYR* 1.3 82.1 + - + +
189C LEU* 3.5 31.5 - - + +
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Residues in contact with TYR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.0 44.2 + - + +
38C THR* 1.3 99.5 - - + +
40C GLY* 1.3 57.6 + - - +
70C ASP 4.6 5.2 - - - +
71C THR* 4.5 5.6 - - + -
72C PRO* 3.7 44.1 - - + +
189C LEU* 4.0 14.8 - - + +
192C ALA* 5.9 0.9 - - + -
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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