Contacts of the helix formed by residues 20 - 42 (chain B) in PDB entry 3LKB
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 THR 20 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 3.7 0.4 - - - +
19B PRO* 1.3 76.0 + - - +
21B SER* 1.3 57.1 + - - +
22B ASP 3.2 3.1 - - - -
23B ALA* 3.0 20.6 + - - +
58B TYR* 3.4 29.0 - - + +
82B TYR* 2.7 42.6 + - - -
151B HIS* 4.0 19.2 + - + +
155B PHE* 4.2 7.0 - - + -
207B VAL* 3.8 13.6 - - + +
393B VAL 3.8 11.7 - - - +
4571B IPA 3.4 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA 3.3 16.2 - - - -
16B ILE 3.4 22.9 - - - -
17B THR* 3.6 8.5 - - - -
18B GLY 2.7 25.7 + - - -
19B PRO 3.2 1.8 + - - -
20B THR* 1.3 71.5 - - - +
22B ASP* 1.3 64.1 + - - +
23B ALA 2.9 7.1 + - - -
24B GLY 3.8 0.2 - - - +
25B ALA* 3.1 24.3 + - - +
4571B IPA 3.3 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER* 1.3 77.7 + - - +
23B ALA* 1.3 55.8 + - - +
26B PRO* 3.3 20.1 - - - +
207B VAL* 4.6 9.2 - - + -
208B ALA* 4.8 9.9 - - + +
209B GLY* 3.4 29.5 + - - +
237B ASP* 4.5 13.7 - - + +
241B LEU* 5.2 11.6 - - - +
286B ASN* 5.1 0.9 + - - -
4571B IPA 2.9 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR 3.0 9.9 + - - +
21B SER 2.9 0.4 - - - -
22B ASP* 1.3 81.2 - - - +
24B GLY* 1.3 63.4 + - - +
25B ALA 3.3 0.9 - - - -
26B PRO* 3.3 4.9 - - - +
27B TYR* 3.2 22.2 + - - +
82B TYR* 3.8 6.7 - - + +
207B VAL* 4.0 12.8 - - + -
232B TYR* 3.6 35.2 - - + +
286B ASN* 3.8 15.9 - - - +
393B VAL 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.5 10.2 - - - -
15B ALA 3.2 17.9 - - - -
16B ILE* 4.5 0.3 - - - -
20B THR 3.2 3.8 + - - -
21B SER 3.3 1.4 + - - -
23B ALA* 1.3 74.7 - - - +
25B ALA* 1.3 55.8 + - - +
27B TYR* 3.5 2.3 - - - +
28B GLY* 2.8 30.0 + - - -
82B TYR* 3.1 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.9 20.8 - - + +
15B ALA 3.5 2.2 + - - -
16B ILE* 3.4 28.7 - - - +
21B SER* 3.1 14.4 + - - +
24B GLY* 1.3 77.5 - - - +
26B PRO* 1.4 66.8 - - + +
28B GLY* 3.8 0.7 - - - -
29B ALA* 2.9 29.3 + - - +
281B PHE* 3.7 11.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER 3.9 0.2 - - - +
22B ASP 3.3 24.2 - - - +
23B ALA 3.3 10.5 - - - +
25B ALA* 1.4 94.3 - - + +
27B TYR* 1.3 62.6 + - - +
29B ALA* 3.5 0.4 + - + -
30B ALA 3.0 17.7 + - - -
237B ASP* 4.9 1.1 - - - +
281B PHE* 3.5 28.2 - - + -
284B SER* 3.7 23.1 - - - +
286B ASN* 3.8 4.9 - - + -
287B TYR* 3.4 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.2 38.1 - + - -
23B ALA 3.2 17.7 + - - +
24B GLY* 3.5 8.5 - - - +
25B ALA 3.2 0.6 - - - -
26B PRO* 1.3 79.7 - - - +
28B GLY* 1.3 60.7 + - - +
30B ALA* 3.2 5.5 + - - +
31B VAL* 3.2 24.0 + - + +
80B LEU* 5.7 1.0 - - + +
81B SER 4.5 0.7 + - - -
82B TYR* 4.9 0.9 - + - -
102B ILE 4.8 0.9 + - - -
103B PRO 3.9 3.3 + - - -
104B ALA* 3.4 42.1 + - + -
122B PRO* 5.3 0.7 - - - +
232B TYR* 4.3 3.1 - + - -
286B ASN* 3.3 12.9 + - + +
289B ASN* 3.5 35.1 + - - -
290B GLY* 3.6 23.4 - - - -
293B ALA* 3.1 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.9 29.2 - - - -
16B ILE* 5.0 3.1 - - - -
24B GLY 2.8 20.1 + - - -
25B ALA 3.8 0.7 - - - -
27B TYR* 1.3 71.2 - - - +
29B ALA* 1.3 65.4 + - - +
31B VAL* 3.3 4.6 + - - +
32B GLU* 3.1 23.4 + - - +
53B VAL* 4.0 10.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
57A GLN* 5.0 0.2 - - - +
16B ILE* 5.8 0.2 - - - +
25B ALA 2.9 17.2 + - - +
26B PRO 3.7 4.7 - - - +
28B GLY* 1.3 76.1 - - - +
30B ALA* 1.3 55.8 + - - +
32B GLU* 3.4 3.2 + - - -
33B ASP* 3.0 34.7 + - - +
277B ARG* 3.4 35.2 + - - +
281B PHE* 4.0 17.7 - - + -
287B TYR* 3.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PRO 3.0 12.0 + - - +
27B TYR 3.2 8.5 + - - +
29B ALA* 1.3 73.0 - - - +
31B VAL* 1.3 61.1 + - - +
33B ASP* 4.5 0.9 - - - +
34B TYR* 2.8 34.0 + - - +
287B TYR* 3.1 43.9 - - + +
290B GLY* 3.6 2.5 - - - -
291B MET* 3.4 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 5.1 10.0 - - + +
12B TRP* 4.2 28.7 - - + -
27B TYR* 3.2 19.4 + - + +
28B GLY* 3.3 6.7 + - - +
30B ALA* 1.3 77.5 - - - +
32B GLU* 1.3 62.7 + - - +
34B TYR* 4.0 1.0 - - - +
35B CYS* 3.1 24.1 + - - +
51B CYS* 4.7 4.9 - - - -
53B VAL* 4.0 17.3 - - + -
80B LEU* 3.8 27.6 - - + -
290B GLY 4.0 13.9 + - - +
294B ALA* 4.1 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 6.1 1.0 - - - +
28B GLY 3.1 12.3 + - - +
29B ALA* 3.6 9.2 - - - +
31B VAL* 1.3 77.0 - - - +
33B ASP* 1.3 59.9 + - - +
35B CYS* 3.2 1.9 - - - +
36B LYS* 3.0 51.7 + - + -
51B CYS* 3.8 18.1 - - + +
53B VAL* 4.0 23.3 + - + +
277B ARG* 3.4 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 3.0 15.1 + - - +
30B ALA* 4.0 2.7 - - - +
32B GLU* 1.3 72.3 - - - +
34B TYR* 1.3 67.9 + - - +
35B CYS 3.0 1.1 - - - -
36B LYS* 3.2 6.9 + - - +
37B TRP* 2.9 24.1 + - - +
271B ILE* 3.5 20.2 - - + -
275B TYR* 3.7 25.8 - - + +
277B ARG* 2.6 49.1 + - - +
287B TYR* 2.6 21.6 + - - +
291B MET* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 2.8 22.9 + - - +
33B ASP* 1.3 72.8 - - - +
35B CYS* 1.3 56.3 + - - +
37B TRP* 3.3 10.7 + + - +
38B ALA* 2.8 25.1 + - - +
43B LEU* 3.7 20.3 - - + +
267B LEU* 4.0 23.0 - - + +
271B ILE* 3.9 13.1 - - + +
291B MET* 3.6 24.2 - - + +
294B ALA* 3.8 18.8 - - + -
295B ALA* 3.5 43.8 + - + +
298B VAL* 3.8 26.9 - - + +
329B PHE* 5.5 2.6 - - - -
333B PHE* 5.1 1.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.7 33.9 - - + -
31B VAL 3.1 13.1 + - - +
32B GLU 3.2 11.2 - - - +
34B TYR* 1.3 74.7 - - - +
36B LYS* 1.3 71.8 + - - +
37B TRP 3.0 1.8 + - - -
38B ALA* 3.2 15.9 + - - +
39B ASN* 3.2 16.6 + - - -
49B PHE* 3.9 21.0 - - - +
51B CYS* 3.5 32.3 - - - -
294B ALA* 5.4 0.6 - - - +
298B VAL* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLU* 3.0 50.7 + - + +
33B ASP* 3.2 7.8 + - - +
35B CYS* 1.3 78.7 - - - +
37B TRP* 1.3 56.9 + - - +
39B ASN* 3.2 14.6 + - - +
40B GLU* 2.9 25.3 + - - +
49B PHE 4.9 4.9 + - - -
51B CYS* 2.8 34.9 - - - +
275B TYR* 3.4 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP 2.9 17.4 + - - +
34B TYR* 3.4 13.0 - + - +
35B CYS 3.0 0.2 - - - -
36B LYS* 1.3 75.6 - - - +
38B ALA* 1.3 66.4 + - - +
40B GLU* 3.1 6.9 + - + -
41B ARG* 3.0 66.7 + - + +
43B LEU* 4.3 18.6 - - + +
267B LEU* 3.8 25.4 - - + +
270B GLU* 3.4 31.6 - - + -
271B ILE* 3.5 33.7 - - + -
274B LYS* 4.3 21.5 - - + -
275B TYR* 3.4 15.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR 2.8 16.9 + - - +
35B CYS* 3.5 8.1 - - - +
37B TRP* 1.3 72.9 - - - +
39B ASN* 1.3 59.2 + - - +
42B LYS* 2.9 24.4 + - - -
43B LEU* 3.1 34.5 + - + -
49B PHE* 3.5 33.6 - - + -
298B VAL* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B CYS 3.2 12.3 + - - -
36B LYS* 3.2 17.6 + - - +
37B TRP 3.1 0.8 - - - -
38B ALA* 1.3 74.7 - - - +
40B GLU* 1.3 65.7 + - - +
41B ARG 3.1 1.2 + - - -
42B LYS* 3.2 25.9 + - - +
47B VAL 4.5 1.7 - - - +
48B VAL* 3.8 14.0 - - + +
49B PHE* 2.9 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS 2.9 11.0 + - - +
37B TRP* 3.1 14.6 + - + +
39B ASN* 1.3 73.7 - - - +
41B ARG* 1.3 70.4 + - + +
42B LYS* 4.1 8.0 - - - +
274B LYS* 3.8 31.3 + - + +
275B TYR* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TRP* 3.0 63.3 + - + +
40B GLU* 1.3 84.7 - - + +
42B LYS* 1.3 78.6 + - - +
43B LEU* 4.3 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLN* 5.0 11.4 + - - -
38B ALA 2.9 11.0 + - - -
39B ASN* 3.2 20.1 + - - +
40B GLU 4.1 6.7 - - - +
41B ARG* 1.3 87.6 - - - +
43B LEU* 1.3 65.9 + - - +
44B VAL 3.2 13.4 + - - +
45B PRO* 4.3 8.6 - - + +
46B GLY 5.8 0.9 - - - +
47B VAL 5.7 3.4 - - - +
48B VAL* 6.0 3.2 - - - +
----------------------------------------------------------
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