Contacts of the helix formed by residues 23 - 40 (chain C) in PDB entry 4LQL
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 ALA 23 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.2 30.3 - - + +
20C GLY* 3.9 1.9 + - - -
21C PRO 3.4 0.4 - - - -
22C GLU* 1.3 79.4 - - - +
24C LEU* 1.3 61.2 + - - +
25C ALA 3.6 0.2 + - - -
26C GLU* 3.6 11.7 + - - +
27C VAL 4.1 0.3 + - - -
122C ASN* 5.3 12.8 - - + -
123C LEU* 3.3 28.8 - - + +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 3.2 31.4 - - - +
16C GLN 4.3 6.5 - - - +
17C PRO 5.5 2.2 - - - +
19C TYR* 3.7 25.8 - - + +
20C GLY 3.3 21.4 + - - +
21C PRO 3.9 2.7 - - - +
23C ALA* 1.3 75.0 - - - +
25C ALA* 1.3 59.6 + - - +
26C GLU 3.1 5.6 - - - -
27C VAL* 3.0 40.7 - - + +
28C GLU* 3.2 12.7 + - - +
53C VAL* 5.2 7.9 - - + -
55C THR* 5.3 7.9 - - + -
82C THR* 5.3 0.2 - - - +
123C LEU* 5.0 2.9 - - + -
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PRO 3.1 16.0 + - - +
22C GLU* 3.1 33.8 + - - +
24C LEU* 1.3 78.6 - - - +
26C GLU* 1.3 56.9 + - - +
28C GLU* 3.4 9.6 - - - +
29C LYS* 3.0 33.2 + - + +
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLU* 3.6 11.2 + - + +
23C ALA* 3.6 5.7 + - - +
24C LEU 3.1 0.8 - - - -
25C ALA* 1.3 78.1 - - + +
27C VAL* 1.3 53.8 + - - +
28C GLU 3.1 1.1 - - - -
29C LYS* 2.8 6.3 + - - +
30C ASP* 2.3 47.0 + - - -
123C LEU* 3.6 21.3 - - + -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 5.0 4.8 - - + +
15C SER* 5.2 1.3 - - - -
24C LEU* 3.0 45.3 - - + +
26C GLU* 1.3 76.8 - - - +
28C GLU* 1.3 53.6 + - + +
30C ASP* 3.8 7.7 - - - +
31C ALA* 2.6 35.9 + - - +
53C VAL* 4.4 19.1 - - + -
81C HIS* 3.2 42.8 - - + +
82C THR* 4.4 4.5 - - + +
123C LEU* 3.4 22.6 - - + +
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 5.9 2.2 - - - -
24C LEU 3.2 20.2 + - - +
25C ALA* 3.4 15.5 - - + +
27C VAL* 1.3 78.2 - - + +
29C LYS* 1.3 63.8 + - + +
30C ASP 3.1 1.8 - - - -
31C ALA* 4.2 4.9 - - - -
32C ARG* 3.1 37.8 + - + +
53C VAL* 6.1 4.9 - - + -
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Residues in contact with LYS 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ALA* 3.0 22.9 - - + +
26C GLU* 2.8 7.2 + - + +
28C GLU* 1.3 82.3 - - + +
30C ASP* 1.3 61.7 + - - +
32C ARG* 5.3 1.3 - - - -
33C LYS* 3.0 27.5 - - - +
107C PHE* 5.2 1.6 - - - -
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Residues in contact with ASP 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLU* 2.3 44.6 + - - +
27C VAL* 3.8 8.1 - - - +
29C LYS* 1.3 73.7 - - - +
31C ALA* 1.3 54.2 + - - +
33C LYS* 3.2 6.5 + - - +
34C LEU* 2.5 37.5 + - + +
79C TRP* 6.2 1.3 - - + -
81C HIS* 4.3 16.6 - - + +
107C PHE* 3.2 46.2 - - + -
123C LEU* 4.8 2.7 - - - -
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 5.6 4.9 - - + -
13C VAL* 4.5 17.0 - - + -
27C VAL 2.6 23.0 + - - +
28C GLU* 3.6 5.6 + - - +
30C ASP* 1.3 68.9 - - - +
32C ARG* 1.3 54.8 + - - +
33C LYS 2.9 3.6 - - - -
34C LEU* 2.5 28.9 + - - +
35C VAL* 2.5 27.0 + - + +
50C PHE* 4.0 17.7 - - + -
79C TRP* 6.2 2.5 - - - -
81C HIS* 6.4 0.4 - - - -
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Residues in contact with ARG 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU* 3.1 21.8 + - + +
29C LYS* 5.3 1.1 - - - -
31C ALA* 1.3 79.7 - - + +
33C LYS* 1.3 56.4 + - + +
35C VAL* 4.2 7.4 - - - +
36C ASP* 3.1 36.2 + - - +
50C PHE* 4.2 19.3 - - + -
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Residues in contact with LYS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 3.0 26.4 + - - +
30C ASP* 3.2 9.5 + - - +
31C ALA 2.9 0.2 - - - -
32C ARG* 1.3 80.3 - - + +
34C LEU* 1.3 56.3 + - - +
37C GLY* 3.8 7.9 + - - -
107C PHE* 4.8 11.7 - - + -
151C TRP* 2.9 24.4 - - + -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 5.3 8.1 - - + -
30C ASP* 2.5 16.0 + - + +
31C ALA* 2.5 17.5 + - - +
33C LYS* 1.3 70.3 - - - +
35C VAL* 1.3 67.8 + - + +
37C GLY 3.2 4.7 + - - -
38C LEU* 3.5 11.1 - - - +
79C TRP* 5.0 12.6 - - + -
107C PHE* 5.7 1.1 - - + -
151C TRP* 3.1 49.9 - - + +
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 3.6 32.5 - - + -
31C ALA* 2.5 29.9 + - - +
32C ARG* 4.4 1.8 - - - -
34C LEU* 1.3 70.1 - - - +
36C ASP* 1.3 55.8 + - - +
38C LEU* 2.6 39.9 + - - +
39C ASN* 2.7 13.4 - - - +
48C VAL* 3.6 28.7 - - + -
50C PHE* 3.5 43.3 - - + +
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Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 3.1 25.7 + - - +
35C VAL* 1.3 82.3 - - - +
37C GLY* 1.3 58.9 + - - +
38C LEU 3.0 2.1 + - - -
39C ASN* 3.6 16.8 - - - -
40C LYS* 3.7 29.6 + - + +
50C PHE* 6.1 1.3 - - - -
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Residues in contact with GLY 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 LYS 3.8 6.0 + - - -
34C LEU 3.2 11.1 + - - -
35C VAL 2.9 2.6 + - - -
36C ASP* 1.3 77.1 - - - +
38C LEU* 1.3 65.0 + - - +
40C LYS* 4.8 2.5 - - - -
41C GLY 5.2 0.9 + - - -
42C GLY* 4.3 12.1 + - - -
151C TRP* 4.0 17.1 - - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 4.0 28.7 - - + -
34C LEU 3.5 12.8 - - - +
35C VAL* 2.6 22.0 + - - +
37C GLY* 1.3 77.4 - - - +
39C ASN* 1.3 66.5 + - - +
40C LYS 3.3 2.1 + - - -
42C GLY* 3.6 16.8 - - - -
44C LEU* 3.3 39.9 - - + +
48C VAL* 5.2 3.6 - - + -
103C LEU* 6.6 0.2 - - + -
151C TRP* 3.7 33.0 - - + +
157C GLN* 3.9 20.4 - - + -
160C ILE* 5.1 14.1 - - + -
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Residues in contact with ASN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 2.7 23.0 - - - +
36C ASP* 3.9 18.6 + - - +
38C LEU* 1.3 72.3 - - - +
40C LYS* 1.3 70.1 + - + +
44C LEU* 4.0 13.6 + - - +
46C TYR 4.5 3.9 - - - -
47C PRO* 4.1 7.7 - - + +
48C VAL* 3.0 51.1 + - - +
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Residues in contact with LYS 40 (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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36C ASP* 3.7 21.4 + - + +
37C GLY 5.4 1.1 - - - -
38C LEU 3.3 1.2 - - - -
39C ASN* 1.3 91.2 - - + +
41C GLY* 1.3 61.1 + - - +
42C GLY 2.9 10.1 + - - -
43C LYS* 3.5 8.5 + - - -
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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
------------------------------------------------------------
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