Contacts of the helix formed by residues 18 - 30 (chain D) in PDB entry 1L3C
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 18 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ASP* 3.5 12.1 - - - +
16D PRO 3.3 2.8 + - - -
17D THR* 1.3 74.7 - - - +
19D MSE 1.3 66.5 + - - +
20D GLU* 3.9 5.6 - - - +
21D VAL* 2.9 29.3 + - + +
22D ARG 3.1 9.7 + - - -
161D ILE* 4.4 8.1 - - + -
163D ARG* 3.5 16.2 - - - +
176D ARG* 4.9 13.2 - - + -
179D VAL* 5.9 3.3 - - + +
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Residues in contact with MSE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 5.0 5.8 - - - -
27A CYS* 3.9 16.8 - - - -
28A LEU* 4.8 16.8 - - + -
1D MSE 3.0 39.9 - - + +
2D ILE 3.8 10.1 - - - +
3D PRO* 3.3 30.5 - - + -
4D ASP* 3.0 21.6 + - - +
17D THR 3.3 0.2 + - - -
18D ALA* 1.3 71.1 - - - +
20D GLU* 1.3 65.0 + - - +
22D ARG* 3.2 16.7 + - - +
23D CYS* 2.9 30.4 + - - +
163D ARG* 3.7 4.2 - - - +
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Residues in contact with GLU 20 (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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24A LEU* 3.6 36.5 - - + +
157A THR* 3.5 18.9 + - + +
159A LEU* 4.2 5.6 - - + -
183A TYR* 5.5 1.0 + - - -
18D ALA* 3.9 4.3 - - - +
19D MSE 1.3 80.0 + - - +
21D VAL* 1.3 60.7 + - - +
23D CYS* 3.4 8.7 - - - +
24D LEU* 3.4 18.9 + - - +
159D LEU* 4.3 7.2 - - + +
161D ILE* 3.6 35.0 - - + +
163D ARG* 2.8 43.9 + - - -
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Residues in contact with VAL 21 (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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17D THR* 3.5 22.2 - - + -
18D ALA* 2.9 16.0 + - + +
20D GLU* 1.3 75.8 - - - +
22D ARG* 1.3 61.5 + - - +
23D CYS 3.1 1.6 - - - -
24D LEU* 3.0 4.9 + - - +
25D ILE* 2.9 39.4 + - + +
133D THR* 5.3 0.4 - - - +
159D LEU* 4.4 13.2 - - + -
161D ILE* 4.1 19.7 - - + -
179D VAL* 4.0 31.0 - - + -
181D LEU* 4.0 20.9 - - + -
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Residues in contact with ARG 22 (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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1D MSE 3.8 15.5 - - - +
2D ILE 2.8 29.7 + - - -
4D ASP* 2.9 27.7 + - - +
7D PHE* 3.6 20.6 - - - -
16D PRO* 4.6 1.0 - - - +
17D THR* 2.9 33.8 + - + +
18D ALA 3.1 6.5 + - - +
19D MSE 3.5 16.3 - - - +
21D VAL* 1.3 75.9 - - - +
23D CYS* 1.3 62.1 + - - +
25D ILE* 3.3 8.8 + - - +
26D MSE 3.1 28.2 + - - +
46D GLY* 3.6 33.8 - - - -
47D VAL* 4.1 7.4 - - + +
50D GLU* 3.0 28.5 + - + -
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Residues in contact with CYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A CYS* 3.0 44.1 - - + -
24A LEU* 3.7 8.1 - - + +
27A CYS* 3.1 37.0 - - + -
1D MSE 4.0 13.2 - - - -
19D MSE 2.9 17.1 + - - +
20D GLU* 3.4 11.2 - - - +
22D ARG* 1.3 78.9 - - - +
24D LEU* 1.3 60.5 + - - +
26D MSE 3.3 4.2 + - - +
27D CYS 3.2 10.7 + - - -
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Residues in contact with LEU 24 (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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19A MSE 5.2 3.6 - - - -
20A GLU* 3.7 44.9 - - + +
23A CYS* 3.8 13.2 - - + -
20D GLU 3.4 9.3 + - - +
21D VAL* 3.0 8.8 + - - +
23D CYS* 1.3 76.6 - - - +
25D ILE* 1.3 66.8 + - - +
27D CYS* 3.1 7.4 + - + -
28D LEU* 3.0 42.2 + - + +
157D THR* 4.2 15.0 - - + -
159D LEU* 4.0 17.9 - - + -
181D LEU* 3.7 23.1 - - + -
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Residues in contact with ILE 25 (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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17D THR* 4.6 3.6 - - + -
21D VAL* 2.9 31.7 + - + +
22D ARG* 3.3 9.4 + - - +
24D LEU* 1.3 76.6 - - - +
26D MSE 1.3 63.5 + - - +
28D LEU* 3.2 5.0 + - - +
29D ALA* 2.9 30.4 + - + +
47D VAL* 3.9 30.5 - - + -
51D LEU* 6.4 0.4 - - + -
105D VAL* 4.0 31.2 - - + -
131D ILE* 3.9 12.9 - - + +
133D THR* 4.0 20.2 - - - +
181D LEU* 4.0 19.5 - - + -
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Residues in contact with MSE 26 (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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1D MSE 4.5 4.3 - - + -
22D ARG 3.1 17.8 + - - +
23D CYS* 3.6 9.0 - - - +
25D ILE* 1.3 81.6 - - - +
27D CYS* 1.3 63.2 + - - +
29D ALA* 4.4 1.3 - - - -
30D GLU* 3.1 18.0 + - - -
31D PRO* 3.1 32.4 - - + +
47D VAL* 5.1 2.0 - - - +
50D GLU* 3.3 46.0 - - + +
51D LEU* 3.7 25.4 - - + -
54D ARG* 3.3 52.2 + - - +
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Residues in contact with CYS 27 (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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1A MSE 3.3 45.4 + - + +
19A MSE 4.0 22.0 - - - -
23A CYS* 3.0 34.8 - - - -
23D CYS 3.2 2.0 + - - -
24D LEU* 3.1 10.8 + - - +
26D MSE 1.3 80.0 - - - +
28D LEU* 1.3 61.7 + - - +
30D GLU* 3.4 18.9 + - - +
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Residues in contact with LEU 28 (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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19A MSE 5.2 12.6 - - + -
24D LEU* 3.0 34.8 + - + +
25D ILE* 3.8 2.9 - - - +
27D CYS* 1.3 75.0 - - - +
29D ALA* 1.3 65.1 + - - +
30D GLU* 3.6 9.1 + - - +
129D ARG* 4.0 13.0 - - - +
131D ILE* 4.1 16.8 - - + +
157D THR* 6.1 0.2 - - - -
181D LEU* 4.1 23.3 - - + -
183D TYR* 3.7 57.0 - - + +
186D VAL* 4.5 4.5 - - - +
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Residues in contact with ALA 29 (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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25D ILE* 2.9 22.0 + - + +
26D MSE 3.9 4.7 - - - +
28D LEU* 1.3 76.0 - - - +
30D GLU* 1.3 55.4 + - - +
31D PRO* 3.5 12.5 - - + -
51D LEU* 5.1 4.0 - - + -
103D ILE* 3.9 23.2 - - + +
105D VAL* 5.4 0.2 - - + -
129D ARG* 2.6 41.4 + - - +
131D ILE* 3.7 17.2 - - + +
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Residues in contact with GLU 30 (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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1A MSE 4.1 19.6 + - - +
26D MSE 3.1 4.9 + - - -
27D CYS 3.4 17.4 - - - +
28D LEU 3.3 2.9 - - - +
29D ALA* 1.3 76.4 - - - +
31D PRO* 1.3 74.2 - - - +
32D GLY* 3.3 2.1 + - - -
35D ASP* 3.9 0.7 - - - +
129D ARG* 3.0 20.9 + - - +
186D VAL* 3.3 42.9 - - - +
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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