Contacts of the helix formed by residues 11 - 24 (chain A) in PDB entry 3LRB
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 GLY 11 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS 4.1 0.2 + - - -
10A VAL* 1.3 85.0 - - - +
12A LEU* 1.3 67.2 + - - -
13A ILE 3.3 2.5 - - - -
14A PRO* 3.0 18.2 - - - +
15A VAL* 3.0 16.4 - - - +
217A VAL* 4.9 1.3 - - - -
218A LYS* 3.7 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 1.3 68.8 - - - -
13A ILE* 1.3 68.4 + - + +
15A VAL* 3.0 6.4 + - - +
16A THR* 2.9 47.4 + - + +
218A LYS* 5.1 0.8 - - - +
223A ASN* 3.2 59.1 + - - +
226A ILE* 3.5 36.1 - - + -
227A ALA* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 1.3 86.5 - - + +
14A PRO* 1.3 71.6 - - + +
16A THR* 3.7 7.5 + - - +
17A LEU* 3.3 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.7 12.6 - - + -
11A GLY* 3.0 21.8 - - - +
13A ILE* 1.3 88.1 - - + +
15A VAL* 1.3 58.5 + - - +
17A LEU* 3.8 5.4 + - + +
18A MET* 3.3 18.2 + - - +
148A THR* 3.1 38.1 + - - +
149A ARG* 5.2 12.8 - - + +
151A GLN* 5.2 0.2 - - - +
152A ALA* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.6 15.9 - - + -
11A GLY 3.0 16.8 - - - +
12A LEU* 3.0 6.3 + - - +
14A PRO* 1.3 74.8 - - - +
16A THR* 1.3 61.9 + - - +
17A LEU 3.0 1.6 - - - -
18A MET* 2.9 13.1 + - + +
19A VAL* 2.8 37.0 + - + +
148A THR* 5.8 0.7 - - - -
209A SER 6.0 0.2 - - - -
210A ALA* 4.6 8.3 - - + -
213A ALA* 5.1 3.6 - - + -
217A VAL* 3.6 44.0 - - + -
224A VAL* 5.8 0.4 - - - -
227A ALA* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 2.9 34.2 + - + +
13A ILE* 3.7 10.6 + - - +
15A VAL* 1.3 75.5 - - - +
17A LEU* 1.3 62.3 + - - +
19A VAL* 3.7 4.0 - - - +
20A SER* 2.8 31.0 + - - -
226A ILE* 4.4 3.8 - - + +
227A ALA* 3.3 37.5 - - + +
230A GLY* 5.0 3.4 - - - -
231A GLY* 3.8 8.7 - - - -
234A ILE* 5.1 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.3 28.6 + - + +
14A PRO 3.9 5.4 - - - +
15A VAL 3.0 0.4 - - - -
16A THR* 1.3 84.6 + - - +
18A MET* 1.3 52.5 + - - +
20A SER* 3.6 8.1 + - - +
21A GLY* 2.7 32.1 + - - -
151A GLN* 4.9 1.3 - - - -
152A ALA* 3.7 37.9 - - + +
155A THR* 3.5 24.8 + - - +
156A VAL* 4.3 20.6 - - + +
159A LEU* 5.8 7.9 - - + -
234A ILE* 5.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 3.3 10.3 + - - +
15A VAL* 2.9 17.2 + - + +
17A LEU* 1.3 77.0 - - - +
19A VAL* 1.3 60.0 + - + +
21A GLY 3.0 7.5 + - - +
22A ASN* 2.8 44.4 + - - +
147A ILE* 4.8 0.4 - - + -
148A THR* 3.7 30.7 - - - +
151A GLN* 4.1 17.4 - - + +
209A SER* 4.9 6.5 - - - +
213A ALA* 5.9 3.1 - - - -
292A GLY* 3.7 20.4 - - - +
295A LEU* 3.5 33.4 - - + -
296A LEU* 4.1 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 2.8 24.1 + - + +
16A THR 3.7 4.3 - - - +
18A MET* 1.3 73.5 - - + +
20A SER* 1.3 63.6 + - - +
21A GLY 3.4 0.2 + - - -
23A ILE* 2.7 38.3 - - + +
207A VAL* 4.6 7.6 - - - +
209A SER* 3.5 15.9 - - - +
210A ALA* 3.4 35.4 - - + +
227A ALA* 3.8 15.7 - - + +
228A THR* 3.7 29.2 - - - +
231A GLY* 4.2 3.4 - - - -
232A VAL* 4.7 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR 2.8 17.7 + - - -
17A LEU* 3.9 9.9 - - - -
19A VAL* 1.3 77.0 - - - +
21A GLY* 1.3 58.6 + - - +
23A ILE* 3.5 3.0 + - - +
24A MET* 2.8 40.3 + - - +
159A LEU* 6.0 0.7 - - - +
231A GLY* 3.4 22.1 + - - -
234A ILE* 3.0 35.1 - - - +
235A ALA* 4.0 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 2.7 20.1 + - - -
18A MET 3.0 3.0 + - - -
20A SER* 1.3 76.5 - - - +
22A ASN* 1.3 68.3 + - - +
24A MET* 4.1 10.0 - - - +
25A GLY* 4.5 3.6 - - - -
151A GLN* 4.0 3.0 + - - -
155A THR* 3.8 28.3 - - - +
285A GLY 4.4 2.1 - - - +
289A SER* 4.1 11.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 2.8 35.9 + - - +
21A GLY* 1.3 81.0 + - - +
23A ILE* 1.3 74.7 + - + +
24A MET 3.1 2.9 + - - -
25A GLY* 3.9 8.1 - - - -
26A SER* 4.4 4.0 + - - -
151A GLN* 3.8 13.1 + - - +
205A ILE 4.5 2.7 - - - +
206A GLY* 5.4 0.2 - - - -
209A SER* 3.8 15.7 - - - +
289A SER* 4.4 7.1 + - - -
292A GLY* 4.1 6.6 - - - -
293A TRP* 2.9 44.8 + - + +
296A LEU* 4.0 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 2.7 31.0 - - + +
20A SER 3.8 1.8 - - - +
22A ASN* 1.3 82.8 - - + +
24A MET* 1.3 62.9 + - - +
25A GLY 3.4 0.9 + - - -
203A SER 4.7 1.6 - - - +
204A PHE* 3.9 23.3 - - + +
205A ILE 3.5 18.0 - - - +
206A GLY* 3.1 34.3 - - - +
207A VAL* 3.4 18.2 - - + +
209A SER* 4.1 4.0 - - - +
231A GLY 5.6 0.2 - - - +
232A VAL* 5.5 2.5 - - + -
235A ALA* 3.3 30.5 - - + -
239A TYR* 3.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 2.8 25.1 + - - +
21A GLY* 4.3 7.2 - - - +
22A ASN 3.1 3.6 - - - -
23A ILE* 1.3 82.3 - - - +
25A GLY* 1.3 57.8 + - - +
28A VAL* 2.8 27.3 + - + +
155A THR* 6.1 2.9 - - + -
158A ALA* 6.3 2.9 - - + -
159A LEU* 3.6 25.4 - - + -
162A ILE* 3.8 18.6 - - + -
234A ILE* 5.0 1.1 - - + -
235A ALA* 4.2 16.4 - - - +
238A CYS* 3.2 43.5 - - + -
239A TYR* 3.1 17.0 + - - -
----------------------------------------------------------
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