Contacts of the helix formed by residues 18 - 30 (chain A) in PDB entry 1L3B
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ASP* 3.7 10.5 - - - -
16A PRO 3.4 2.2 + - - -
17A THR* 1.3 76.1 - - - +
19A MSE 1.3 60.2 + - - +
20A GLU* 4.0 12.1 - - - +
21A VAL* 3.0 23.7 + - + +
22A ARG 2.8 24.1 + - - -
161A ILE* 4.4 7.2 - - + -
163A ARG* 4.4 9.4 - - - +
176A ARG* 4.9 12.1 - - + -
179A VAL* 5.5 4.0 - - + +
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Residues in contact with MSE 19 (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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1A MSE 3.4 44.0 - - + +
2A ILE 4.2 0.2 - - - +
3A PRO* 3.9 19.5 - - + -
4A ASP* 3.0 23.1 + - - +
18A ALA* 1.3 72.2 - - - +
20A GLU* 1.3 68.7 + - - +
22A ARG* 2.9 24.9 + - - +
23A CYS* 2.7 32.2 + - - +
163A ARG* 5.8 1.1 - - - +
24D LEU* 4.7 17.0 - - - -
27D CYS* 5.4 5.4 - - - +
28D LEU* 4.7 19.7 - - + -
183D TYR* 5.9 2.2 - - - +
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Residues in contact with GLU 20 (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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18A ALA* 4.0 3.1 - - - +
19A MSE 1.3 85.4 + - - +
21A VAL* 1.3 59.3 + - - +
23A CYS* 3.5 9.2 - - - +
24A LEU* 3.3 20.8 + - - +
159A LEU* 4.3 7.2 - - + +
161A ILE* 3.2 37.2 - - + +
163A ARG* 3.6 28.1 + - - -
24D LEU* 3.8 32.8 - - + +
157D THR* 3.2 26.3 + - + +
159D LEU* 4.4 7.9 - - + -
183D TYR* 5.6 0.5 + - - -
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Residues in contact with VAL 21 (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 THR* 3.4 19.1 - - + -
18A ALA* 3.0 25.7 + - + +
20A GLU* 1.3 74.4 - - - +
22A ARG* 1.3 60.4 - - - +
24A LEU* 3.1 4.2 + - - +
25A ILE* 2.8 37.0 + - + +
133A THR* 4.5 1.6 - - + -
159A LEU* 4.6 11.9 - - + -
161A ILE* 4.3 10.8 - - + -
179A VAL* 3.9 41.1 - - + -
181A LEU* 3.9 23.1 - - + -
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Residues in contact with ARG 22 (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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1A MSE 3.6 19.7 - - + +
2A ILE 2.8 30.5 + - - -
4A ASP* 2.8 31.3 + - - +
7A PHE* 3.6 19.5 - - - -
16A PRO* 4.9 1.2 - - - +
17A THR* 2.8 30.4 + - + +
18A ALA 2.8 10.1 + - - +
19A MSE 3.3 20.5 - - - +
21A VAL* 1.3 75.2 - - - +
23A CYS* 1.3 63.9 + - - +
25A ILE* 3.4 9.7 + - - +
26A MSE 3.2 28.4 + - - +
46A GLY* 3.8 28.2 - - - -
47A VAL* 4.4 10.8 - - + +
50A GLU* 3.6 23.4 + - + -
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Residues in contact with CYS 23 (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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1A MSE 3.7 9.1 - - - -
19A MSE 2.7 16.7 + - + +
20A GLU* 3.5 9.6 - - - +
22A ARG* 1.3 76.7 - - - +
24A LEU* 1.3 57.8 + - - +
26A MSE 3.1 7.4 + - - +
27A CYS* 3.0 22.5 + - - -
20D GLU 5.3 0.2 - - - -
23D CYS* 3.1 30.5 - - - -
24D LEU* 3.6 18.6 - - + -
27D CYS* 2.8 39.7 - - + -
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Residues in contact with LEU 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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20A GLU 3.3 12.0 + - - +
21A VAL 3.1 4.6 + - - +
23A CYS* 1.3 76.3 - - - +
25A ILE* 1.3 65.9 + - - +
27A CYS* 3.6 1.1 - - + -
28A LEU* 3.1 37.9 + - + +
157A THR* 4.2 12.8 - - + -
159A LEU* 3.7 21.3 - - + -
181A LEU* 3.4 25.4 - - + -
19D MSE 4.2 21.3 - - - -
20D GLU* 4.0 31.6 - - + +
23D CYS* 3.6 16.2 - - - -
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Residues in contact with ILE 25 (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 THR* 4.4 4.0 - - + +
21A VAL* 2.8 36.1 + - + +
22A ARG* 3.6 7.0 - - - +
23A CYS 3.2 0.2 - - - -
24A LEU* 1.3 77.1 - - - +
26A MSE 1.3 65.8 + - - +
28A LEU* 4.8 2.9 - - - -
29A ALA* 3.1 29.0 + - + +
47A VAL* 3.8 31.2 - - + -
51A LEU* 6.5 0.2 - - + -
105A VAL* 4.4 23.3 - - + -
131A ILE* 3.7 20.8 - - + +
133A THR* 4.0 17.5 - - - +
181A LEU* 3.9 18.2 - - + -
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Residues in contact with MSE 26 (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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1A MSE 4.0 6.5 - - + -
22A ARG 3.2 14.1 + - - +
23A CYS 3.1 9.4 + - - +
25A ILE* 1.3 84.1 - - + +
27A CYS* 1.3 66.2 + - - +
29A ALA* 4.6 1.1 - - - -
30A GLU* 2.9 20.1 + - - -
31A PRO* 3.3 28.0 - - + +
47A VAL* 5.1 2.0 - - - +
50A GLU* 2.8 43.7 - - + +
51A LEU* 3.7 21.3 - - - +
54A ARG* 3.0 56.5 - - + +
27D CYS* 6.1 0.9 - - - -
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Residues in contact with CYS 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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23A CYS* 3.0 10.1 + - - -
24A LEU* 3.3 9.1 + - + +
26A MSE 1.3 76.5 - - - +
28A LEU* 1.3 56.4 + - - +
30A GLU* 2.8 31.0 - - - +
1D MSE 4.4 21.9 + - + +
19D MSE 4.7 13.6 - - + +
23D CYS* 2.0 58.1 - - + -
26D MSE 6.2 0.2 - - - -
27D CYS* 5.3 3.1 - - - -
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Residues in contact with LEU 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 LEU* 3.1 42.1 + - + +
25A ILE* 4.8 0.4 - - - -
27A CYS* 1.3 78.9 - - - +
29A ALA* 1.3 63.8 + - - +
30A GLU* 3.2 12.5 + - - +
129A ARG* 4.3 8.7 - - - +
131A ILE* 3.9 17.9 - - + -
157A THR* 5.9 0.7 - - - +
181A LEU* 4.1 15.3 - - + -
183A TYR* 3.8 55.0 - - + +
186A VAL* 5.8 0.9 - - - +
19D MSE 4.6 18.8 - - + -
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Residues in contact with ALA 29 (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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25A ILE* 3.1 22.3 + - + +
26A MSE 4.2 4.3 - - - +
28A LEU* 1.3 76.6 - - - +
30A GLU* 1.3 71.5 + - - +
31A PRO* 4.3 5.8 - - + -
51A LEU* 5.5 0.7 - - + -
103A ILE* 3.6 30.9 - - + +
105A VAL* 5.6 0.2 - - + -
129A ARG* 2.9 31.8 + - + +
131A ILE* 3.6 15.3 - - + +
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Residues in contact with GLU 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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26A MSE 2.9 12.3 + - - -
27A CYS 2.8 23.3 - - - +
28A LEU 3.5 8.0 - - - +
29A ALA* 1.3 81.3 - - - +
31A PRO* 1.3 69.7 - - - +
129A ARG* 3.8 4.0 + - - +
186A VAL* 5.4 7.8 - - - +
76C GLN* 3.4 16.5 - - - +
82C ASP* 5.1 11.6 - - - +
1D MSE 3.5 22.7 + - - +
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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