Contacts of the helix formed by residues 27 - 43 (chain D) 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 VAL 27 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D VAL* 5.1 5.4 - - + -
15D SER* 5.8 2.0 - - - -
23D ALA* 3.1 24.7 - - + +
24D LEU* 3.6 22.0 - - + -
25D ALA 2.9 9.6 - - - +
26D GLU* 1.3 83.0 - - - +
28D GLU* 1.3 70.9 + - + +
29D LYS 3.0 2.9 + - - -
30D ASP* 3.1 7.3 + - - +
31D ALA* 2.9 25.7 + - - +
53D VAL* 5.2 9.0 - - + -
81D HIS* 3.7 32.3 + - + +
82D THR* 4.6 17.3 - - + -
123D LEU* 5.6 9.4 - - + -
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Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU 5.2 1.6 - - - +
25D ALA* 3.5 25.1 - - + +
27D VAL* 1.3 84.3 - - + +
29D LYS* 1.3 56.3 + - + +
31D ALA* 3.7 10.5 - - + -
32D ARG* 2.4 48.0 + - + +
50D PHE* 6.5 0.4 - - + -
53D VAL* 5.0 15.7 - - + -
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA 3.4 12.3 + - - +
26D GLU* 5.0 3.4 - - - -
27D VAL 3.0 1.2 - - - -
28D GLU* 1.3 80.7 - - + +
30D ASP* 1.3 58.0 + - - +
31D ALA 3.0 0.2 + - - -
32D ARG* 3.1 6.0 + - + +
33D LYS* 2.6 39.6 + - + +
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Residues in contact with ASP 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D GLU 3.9 19.5 - - - -
27D VAL 3.1 5.1 + - - +
29D LYS* 1.3 78.1 - - - +
31D ALA* 1.3 56.9 + - - +
33D LYS* 3.2 10.4 + - - +
34D LEU* 2.9 31.4 + - - +
79D TRP* 5.2 1.6 - - + -
81D HIS* 4.1 11.4 - - + -
107D PHE* 3.7 30.5 - - + +
124D HIS* 6.2 0.4 - - - -
151D TRP* 4.7 1.2 - - - -
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 5.1 3.8 - - + -
13D VAL* 3.9 28.3 - - + -
27D VAL 2.9 13.4 + - - +
28D GLU* 3.4 13.7 - - + +
30D ASP* 1.3 73.4 - - - +
32D ARG* 1.3 57.3 + - + +
33D LYS 3.0 4.3 - - - -
34D LEU* 2.9 24.1 + - - +
35D VAL* 3.1 21.1 + - + +
50D PHE* 5.2 6.7 - - + -
53D VAL* 5.6 0.4 - - + -
79D TRP* 4.0 9.4 - - + -
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Residues in contact with ARG 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLU* 2.4 40.4 + - + +
29D LYS* 3.8 5.2 - - - +
31D ALA* 1.3 67.0 - - - +
33D LYS* 1.3 57.2 + - - +
35D VAL* 4.3 7.4 - - - -
36D ASP* 3.6 26.3 + - + +
50D PHE* 4.2 20.9 - - + -
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Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS* 2.6 22.9 + - + +
30D ASP* 3.3 12.1 - - - +
31D ALA 3.0 0.2 - - - -
32D ARG* 1.3 73.8 - - - +
34D LEU* 1.3 61.4 + - - +
37D GLY* 3.5 13.1 - - - +
151D TRP* 2.9 29.6 - - + -
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.8 13.5 - - + -
30D ASP 2.9 18.4 + - - +
31D ALA* 2.9 14.6 + - - +
33D LYS* 1.3 76.9 - - - +
35D VAL* 1.3 57.8 + - + +
37D GLY 3.5 0.2 - - - -
38D LEU* 2.7 43.6 + - + +
79D TRP* 4.2 20.9 - - + -
105D THR* 6.2 0.7 - - + -
107D PHE* 5.5 3.4 - - - -
151D TRP* 3.4 38.0 - - + +
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 3.8 24.5 - - + -
31D ALA 3.1 15.6 + - - +
32D ARG* 4.6 2.0 - - - +
34D LEU* 1.3 71.9 - - - +
36D ASP* 1.3 59.1 + - + +
37D GLY 2.8 1.7 + - - -
38D LEU* 2.5 37.4 + - - +
39D ASN* 3.0 8.9 + - - +
48D VAL* 3.2 31.6 - - + +
49D GLU 2.9 28.7 - - - +
50D PHE* 3.6 24.9 - - + +
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Residues in contact with ASP 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ARG 3.6 15.3 + - - +
35D VAL* 1.3 80.9 - - + +
37D GLY* 1.3 57.2 + - - +
39D ASN* 3.1 22.4 + - - +
40D LYS* 3.9 19.8 - - - +
48D VAL 5.4 0.4 - - - -
50D PHE* 6.5 0.2 - - - -
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Residues in contact with GLY 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ARG 4.4 0.2 + - - -
33D LYS* 3.5 19.8 + - - +
34D LEU 3.5 2.1 + - - -
35D VAL 2.8 1.6 + - - -
36D ASP* 1.3 77.6 - - - +
38D LEU* 1.3 63.2 + - - +
39D ASN 3.3 0.7 - - - -
40D LYS* 3.7 11.8 + - - +
41D GLY* 3.8 8.5 + - - -
42D GLY 4.8 0.2 + - - -
151D TRP* 4.2 11.3 - - - -
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Residues in contact with LEU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 5.2 15.0 - - + -
34D LEU* 2.7 21.6 + - + +
35D VAL* 2.5 16.6 + - - +
37D GLY* 1.3 70.7 - - - -
39D ASN* 1.3 55.3 + - - +
42D GLY* 2.9 35.9 + - - +
44D LEU* 4.4 19.6 - - + +
48D VAL* 4.2 23.8 - - + -
151D TRP* 4.5 20.4 - - + -
157D GLN* 4.1 26.9 - - + -
160D ILE* 5.0 13.7 - - + -
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Residues in contact with ASN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D VAL 3.0 3.2 + - - +
36D ASP* 3.1 38.0 + - - +
38D LEU* 1.3 79.0 - - - +
40D LYS* 1.3 65.6 - - + +
41D GLY 3.4 1.2 + - - -
42D GLY 3.9 2.9 + - - -
43D LYS* 4.6 4.3 + - - -
44D LEU* 5.3 5.9 + - - +
47D PRO* 3.5 17.3 - - + +
48D VAL* 2.7 50.9 + - - +
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Residues in contact with LYS 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ASP 3.9 17.5 - - - +
37D GLY* 3.7 7.0 + - - +
38D LEU 3.3 0.6 - - - -
39D ASN* 1.3 83.7 - - + +
41D GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLY 3.8 8.2 + - - -
40D LYS* 1.3 77.9 - - - +
42D GLY* 1.3 71.6 + - - +
43D LYS* 2.7 10.8 + - - +
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Residues in contact with GLY 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLY 4.8 0.2 + - - -
38D LEU* 2.9 29.0 + - - -
39D ASN 3.9 1.2 + - - -
40D LYS 3.8 0.2 - - - -
41D GLY* 1.3 75.8 - - - +
43D LYS* 1.3 72.2 + - - +
44D LEU* 4.0 15.8 - - - +
157D GLN* 4.8 14.3 - - - +
161D ALA* 5.3 0.5 - - - +
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Residues in contact with LYS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASN 4.6 3.8 + - - -
41D GLY 2.7 12.8 + - - +
42D GLY* 1.3 79.1 - - - +
44D LEU* 1.3 65.0 + - - +
161D ALA* 3.6 17.8 - - - +
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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