Contacts of the helix formed by residues 14 - 38 (chain C) in PDB entry 4NE1
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 SER 14 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR* 1.3 72.7 + - - +
16C GLN 3.7 3.5 + - - -
17C GLN* 3.2 34.7 + - - +
18C ARG* 3.5 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C SER* 1.3 81.2 + - - +
16C GLN* 1.3 58.1 + - + +
18C ARG* 3.7 27.4 + - - +
19C LEU* 3.5 40.6 + - + +
17D ARG* 4.0 30.5 + - + -
21D LEU* 5.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C SER* 3.7 2.8 + - - -
15C TYR* 1.3 74.3 - - + +
17C GLN* 1.3 63.9 - - + +
19C LEU* 3.3 19.5 + - + +
20C LYS* 3.1 36.9 + - - +
55C PHE* 3.7 24.2 - - + -
21D LEU* 3.8 23.0 - - + +
22D HIS* 3.4 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C SER* 3.2 39.0 + - - +
15C TYR 3.5 0.4 - - - -
16C GLN* 1.3 76.7 - - + +
18C ARG* 1.3 57.6 + - - +
20C LYS* 3.6 23.8 + - + +
21C ALA* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C SER 3.5 9.7 + - - +
15C TYR* 3.8 33.4 + - - +
16C GLN 3.3 0.4 - - - -
17C GLN* 1.3 76.3 - - - +
19C LEU* 1.3 83.3 + - - +
21C ALA* 3.4 7.1 - - + +
22C ALA* 2.6 57.4 + - - +
13D GLU* 5.0 9.5 + - - -
14D LEU* 4.9 2.8 - - - +
17D ARG* 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR* 3.5 33.6 + - + +
16C GLN* 3.3 17.1 + - + +
18C ARG* 1.3 99.7 - - - +
20C LYS* 1.3 59.9 + - - +
22C ALA* 3.9 4.2 - - - +
23C VAL* 3.0 34.1 + - - +
55C PHE* 3.9 9.9 - - + -
14D LEU* 4.4 10.1 - - + +
17D ARG* 4.9 14.8 - - + -
18D LEU* 4.0 15.5 - - + -
21D LEU* 3.0 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLN* 3.1 27.1 + - - +
17C GLN* 3.6 28.1 - - - +
19C LEU* 1.3 75.3 - - - +
21C ALA* 1.3 59.4 + - - +
23C VAL* 3.5 6.3 + - - +
24C HIS* 2.9 25.1 + - - +
51C SER* 4.7 5.5 - - - +
52C GLU* 6.3 4.9 - - + -
55C PHE* 3.7 46.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLN 3.2 14.9 + - - +
18C ARG* 3.6 8.7 - - + +
20C LYS* 1.3 78.8 - - - +
22C ALA* 1.3 61.7 + - - +
24C HIS* 3.3 22.6 - - + +
25C TYR* 3.4 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG* 2.6 44.3 + - - +
19C LEU 3.9 4.5 - - - +
20C LYS 3.4 0.2 - - - -
21C ALA* 1.3 70.2 - - - +
23C VAL* 1.3 64.9 + - - +
25C TYR* 3.5 8.4 + - - +
26C THR* 3.6 3.8 + - - -
11D ARG* 3.3 30.0 + - - +
14D LEU* 3.9 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU 3.0 21.3 + - - +
20C LYS* 3.6 5.8 - - - +
22C ALA* 1.3 76.1 - - - +
24C HIS* 1.3 55.4 + - - +
25C TYR 3.5 0.2 + - - -
26C THR* 3.5 2.3 + - - -
27C VAL* 3.0 39.3 + - + +
51C SER 3.4 25.8 - - - +
54C THR* 3.5 29.6 - - + -
55C PHE* 3.9 7.4 - - + +
10D PHE* 4.7 1.6 - - + -
14D LEU* 4.0 14.1 - - + -
18D LEU* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LYS 2.9 15.8 + - - +
21C ALA* 3.3 17.7 - - + +
23C VAL* 1.3 75.7 - - - +
25C TYR* 1.3 55.5 + - - +
28C GLY* 3.1 24.4 + - - -
44C LYS* 5.2 8.8 - - + +
47C ILE* 3.8 20.9 - - + +
48C ALA* 3.7 30.2 - - + -
51C SER* 3.1 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA 3.4 8.8 + - - +
22C ALA* 3.9 7.2 - - - +
23C VAL 3.4 0.8 - - - -
24C HIS* 1.3 76.7 - - - +
26C THR* 1.3 64.1 + - - +
28C GLY* 3.5 2.1 + - - -
29C CYS* 3.3 40.0 + - - -
11D ARG* 3.0 41.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ALA 3.6 3.8 + - - -
23C VAL 3.5 5.9 + - - -
24C HIS 3.5 0.2 - - - -
25C TYR* 1.3 76.4 - - - +
27C VAL* 1.3 64.8 + - - +
28C GLY 3.2 1.1 - - - -
29C CYS* 3.3 17.6 + - + +
30C LEU* 3.4 16.1 + - + +
9D GLY 4.8 5.6 - - - +
10D PHE* 3.5 52.7 - - + +
11D ARG* 2.5 36.7 + - - +
14D LEU* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C VAL* 3.0 30.5 + - + +
26C THR* 1.3 75.7 - - - +
28C GLY* 1.3 58.2 + - - +
31C CYS* 3.0 31.0 + - - +
47C ILE* 4.7 2.5 - - + +
50C ILE* 3.5 25.8 - - + -
51C SER* 3.6 19.1 - - - +
54C THR* 3.5 13.2 - - - +
10D PHE* 3.7 8.3 - - + -
46D VAL* 3.3 43.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C HIS 3.1 19.4 + - - -
25C TYR* 3.7 3.4 - - - -
26C THR 3.2 0.2 - - - -
27C VAL* 1.3 75.6 - - - +
29C CYS* 1.3 57.6 + - - +
31C CYS* 3.8 5.6 - - - +
32C GLU* 2.9 34.3 + - - +
47C ILE* 4.5 15.9 - - - +
51C SER* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.3 39.9 + - - -
26C THR* 3.3 10.9 + - + +
28C GLY* 1.3 73.5 - - - +
30C LEU* 1.3 59.2 + - - +
32C GLU* 3.3 5.6 + - - +
33C GLU* 2.9 28.9 + - - +
8D SER* 3.8 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C THR* 3.4 10.9 + - + +
27C VAL 3.9 0.7 - - - +
29C CYS* 1.3 77.4 - - - +
31C CYS* 1.3 57.9 + - - +
33C GLU* 3.1 40.9 - - - +
34C VAL* 3.1 16.0 - - - +
8D SER* 3.6 16.8 - - - +
9D GLY* 5.4 1.1 - - - +
10D PHE* 3.8 33.7 - - + +
43D LYS* 3.8 45.5 - - + +
46D VAL* 3.9 17.7 - - + -
47D VAL* 3.8 18.8 - - + +
50D ALA* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 3.0 30.4 + - - +
28C GLY 4.1 1.6 - - - +
30C LEU* 1.3 75.5 - - - +
32C GLU* 1.3 60.3 + - - +
34C VAL* 3.4 1.0 + - - -
35C ALA 3.2 7.3 + - - -
42C PHE* 3.0 32.6 - - + -
47C ILE* 3.7 22.9 - - + -
50C ILE* 3.5 22.2 - - - -
46D VAL* 4.0 11.9 - - - -
50D ALA* 3.1 32.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLY 2.9 21.1 + - - +
29C CYS* 3.3 5.6 + - - +
31C CYS* 1.3 74.5 - - - +
33C GLU* 1.3 65.2 + - - +
34C VAL 3.2 0.7 - - - -
35C ALA* 3.5 31.1 + - - +
36C LEU* 3.8 9.5 + - - +
41C GLN* 5.3 2.6 - - - +
42C PHE* 4.8 13.7 + - - +
47C ILE* 5.6 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C CYS 2.9 11.5 + - - +
30C LEU* 3.1 28.4 - - - +
32C GLU* 1.3 75.9 - - - +
34C VAL* 1.3 59.6 + - + +
36C LEU* 3.5 21.9 - - - +
37C ASP* 4.0 6.2 + - - +
8D SER* 2.8 38.3 + - - +
43D LYS* 4.9 4.1 + - - -
47D VAL* 4.6 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU 3.1 17.0 + - - +
31C CYS 3.5 7.4 - - - +
32C GLU 3.2 0.6 - - - -
33C GLU* 1.3 73.7 - - + +
35C ALA* 1.3 63.9 + - - +
36C LEU 3.3 2.0 + - - -
37C ASP* 3.4 13.9 + - + +
38C LYS* 3.6 22.6 + - + +
40C MET 4.2 0.9 - - - +
42C PHE* 3.5 19.5 - - + -
47D VAL* 4.2 17.7 - - + +
50D ALA* 3.8 16.8 - - + +
51D VAL* 3.9 30.1 - - + -
54D VAL* 4.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C CYS 3.2 10.0 + - - +
32C GLU* 3.5 34.7 + - - +
34C VAL* 1.3 76.6 - - - +
36C LEU* 1.4 60.0 + - - +
37C ASP 3.6 0.2 + - - -
39C ALA* 3.8 3.1 + - - -
40C MET 3.6 29.7 + - - -
41C GLN* 4.1 15.7 - - + -
42C PHE* 3.6 7.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU 3.8 8.0 + - - +
33C GLU* 3.5 15.6 + - - +
34C VAL 3.3 1.0 - - - -
35C ALA* 1.4 77.6 - - - +
37C ASP* 1.3 63.8 + - + +
38C LYS 3.6 0.4 + - - -
39C ALA* 3.9 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLU 4.0 8.0 + - - +
34C VAL* 3.4 10.6 + - + +
36C LEU* 1.3 80.4 - - + +
38C LYS* 1.3 89.1 + - + +
39C ALA 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 3.6 19.2 + - + +
37C ASP* 1.3 97.9 + - - +
39C ALA* 1.3 70.3 + - - +
40C MET 3.3 2.1 + - - +
51D VAL* 3.7 28.3 - - + +
54D VAL* 3.4 34.1 - - + -
55D ARG* 5.0 9.3 - - + +
58D GLN* 3.9 14.5 + - - +
----------------------------------------------------------
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