Contacts of the helix formed by residues 18 - 30 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 3.5 10.3 - - - +
16B PRO 3.3 3.0 + - - -
17B THR* 1.3 74.0 - - - +
19B MSE 1.3 68.3 + - - +
20B GLU* 3.9 6.1 - - - +
21B VAL* 2.8 29.3 + - + +
22B ARG* 3.1 9.4 + - - +
161B ILE* 4.4 8.1 - - + -
163B ARG* 3.5 16.2 - - - +
176B ARG* 4.9 13.2 - - + -
179B VAL* 5.9 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 3.0 45.2 - - + +
2B ILE 3.6 9.9 - - - +
3B PRO* 3.3 30.5 - - + -
4B ASP* 3.0 22.0 + - - +
18B ALA* 1.3 72.2 - - - +
20B GLU* 1.3 66.8 + - - +
22B ARG* 3.2 13.2 + - - +
23B CYS* 2.9 29.1 + - - +
163B ARG* 3.7 3.1 - - - +
24C LEU* 5.6 5.2 - - - -
27C CYS* 4.4 17.5 - - - -
28C LEU* 5.5 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA* 3.9 4.3 - - - +
19B MSE 1.3 84.6 + - + +
21B VAL* 1.3 61.0 + - - +
23B CYS* 3.4 8.6 - - - +
24B LEU* 3.4 18.7 + - - +
159B LEU* 4.3 7.3 - - + +
161B ILE* 3.6 33.9 - - + +
163B ARG* 2.8 46.2 + - - +
24C LEU* 4.0 34.6 - - + +
157C THR* 3.9 15.7 + - + +
159C LEU* 4.7 4.3 - - + -
183C TYR* 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.6 21.5 - - + -
18B ALA* 2.8 17.5 + - + +
20B GLU* 1.3 73.6 - - - +
22B ARG* 1.3 59.1 - - - +
23B CYS 3.0 1.6 - - - -
24B LEU* 2.9 5.5 + - - +
25B ILE* 2.8 31.8 + - + +
133B THR* 5.3 0.4 - - - +
159B LEU* 4.4 14.1 - - + -
161B ILE* 4.0 19.5 - - + -
179B VAL* 4.1 30.5 - - + -
181B LEU* 4.0 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 3.8 15.1 - - - +
2B ILE 2.9 30.1 + - - -
4B ASP* 2.9 28.7 + - - +
7B PHE* 3.6 20.8 - - - -
16B PRO* 4.6 1.0 - - - +
17B THR* 2.9 35.8 + - + +
18B ALA 3.1 3.3 + - - +
19B MSE 3.2 16.2 + - - +
21B VAL* 1.3 76.0 - - - +
23B CYS* 1.3 63.0 + - - +
25B ILE* 3.8 10.0 - - - +
26B MSE 3.1 29.3 + - - +
46B GLY* 3.6 32.8 - - - -
47B VAL* 4.6 9.0 - - + -
50B GLU* 3.0 29.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 4.0 15.0 - - - -
19B MSE 2.9 17.3 + - - +
20B GLU* 3.4 11.2 - - - +
21B VAL 3.0 0.2 - - - -
22B ARG* 1.3 79.1 - - - +
24B LEU* 1.3 61.9 + - - +
26B MSE 3.3 4.0 + - - +
27B CYS 3.2 16.3 + - - -
23C CYS* 3.6 29.5 - - - -
24C LEU* 4.3 7.0 - - + -
27C CYS* 3.1 41.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU 3.4 9.2 + - - +
21B VAL* 2.9 9.0 + - - +
23B CYS* 1.3 76.0 - - - +
25B ILE* 1.3 66.2 + - - +
27B CYS* 3.1 7.1 + - + -
28B LEU* 2.9 40.2 + - + +
157B THR* 4.2 13.9 - - + +
159B LEU* 4.0 17.9 - - + -
181B LEU* 3.7 23.6 - - + -
19C MSE 5.3 4.9 - - - -
20C GLU* 3.8 38.6 - - + +
23C CYS* 4.1 18.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 4.6 4.3 - - + -
21B VAL* 2.8 37.0 + - + +
22B ARG* 3.8 9.4 - - - +
23B CYS 3.3 0.4 - - - -
24B LEU* 1.3 71.2 - - - +
26B MSE 1.3 62.5 + - - +
28B LEU* 3.2 5.8 + - - +
29B ALA* 2.9 29.9 + - + +
47B VAL* 3.9 31.2 - - + -
51B LEU* 6.4 0.2 - - + -
105B VAL* 4.0 30.5 - - + -
131B ILE* 3.8 12.9 - - + +
133B THR* 4.0 17.5 - - - +
181B LEU* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 4.5 4.3 - - + -
22B ARG 3.1 17.7 + - - +
23B CYS* 3.6 8.7 - - - +
24B LEU 3.2 0.2 - - - -
25B ILE* 1.3 83.1 - - - +
27B CYS* 1.3 61.9 + - - +
29B ALA* 4.4 1.6 - - - -
30B GLU* 3.1 17.7 + - - -
31B PRO* 3.1 42.3 - - + +
47B VAL* 5.1 2.5 - - - +
50B GLU* 3.3 45.1 - - + +
51B LEU* 3.8 24.0 - - + -
54B ARG* 3.4 43.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B CYS 3.2 2.0 + - - +
24B LEU* 3.1 10.8 + - - +
26B MSE 1.3 79.7 - - - +
28B LEU* 1.3 63.6 + - - +
30B GLU* 3.4 18.7 - - - +
1C MSE 3.5 43.9 + - + -
19C MSE 4.4 17.3 - - - -
23C CYS* 3.1 35.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 2.9 35.0 + - + +
25B ILE 3.7 2.9 - - - +
27B CYS* 1.3 75.3 - - - +
29B ALA* 1.3 64.2 + - - +
30B GLU* 3.6 9.6 + - - +
129B ARG* 4.0 14.0 - - - +
131B ILE* 4.1 17.6 - - + +
181B LEU* 4.1 23.3 - - + -
183B TYR* 3.6 56.3 - - + +
186B VAL* 4.6 4.5 - - - +
19C MSE 5.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 2.9 22.0 + - + +
26B MSE 3.9 4.3 - - - +
28B LEU* 1.3 78.1 - - - +
30B GLU* 1.3 55.6 + - - +
31B PRO* 3.5 12.7 - - + -
51B LEU* 5.0 4.5 - - + -
103B ILE* 3.8 22.7 - - + +
105B VAL* 5.4 0.2 - - + -
129B ARG* 2.6 40.5 + - - +
131B ILE* 3.7 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B MSE 3.1 5.1 + - - -
27B CYS 3.4 17.2 - - - +
28B LEU* 3.3 3.3 - - - +
29B ALA* 1.3 76.8 - - - +
31B PRO* 1.3 74.2 - - - +
32B GLY* 3.3 2.3 + - - -
35B ASP* 3.9 0.3 - - - +
129B ARG* 3.1 20.8 + - - +
186B VAL* 3.4 43.8 - - - +
1C MSE 4.2 16.9 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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