Contacts of the helix formed by residues 16 - 29 (chain C) in PDB entry 1N8Z
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 16 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PRO* 3.0 3.5 - - - +
15C ALA* 1.3 82.7 - - - +
17C PRO* 1.3 71.9 - - - +
18C GLU* 3.7 18.7 + - - -
19C THR* 2.4 35.0 + - - -
20C HIS* 3.0 20.1 + - - +
445C LEU* 5.0 3.0 - - - +
447C HIS* 4.2 17.9 + - - -
448C HIS* 4.6 6.1 - - - -
474C THR* 4.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 6.0 4.7 - - + -
14C PRO* 4.6 8.5 - - + +
15C ALA 4.6 0.9 - - - +
16C SER* 1.3 84.2 - - - +
18C GLU* 1.3 76.2 + - + +
20C HIS* 2.7 23.1 + - + +
21C LEU* 3.0 14.8 + - - +
42C TYR* 5.4 8.1 - - + +
44C PRO* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER* 3.7 19.6 - - - -
17C PRO* 1.3 81.0 - - + +
19C THR* 1.3 61.5 + - - +
21C LEU* 3.6 10.6 + - - +
22C ASP* 3.3 19.8 + - - +
448C HIS* 4.3 7.4 + - - -
474C THR* 3.7 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER* 2.4 29.1 + - - -
17C PRO 3.1 0.4 - - - -
18C GLU* 1.3 73.4 - - - +
20C HIS* 1.3 61.2 + - - +
21C LEU 3.2 0.7 - - - -
22C ASP* 3.4 6.9 + - - +
23C MET* 2.9 30.5 + - - +
419C TYR* 4.5 3.1 - - - -
445C LEU* 3.3 21.2 - - + +
472C LEU* 3.0 46.5 - - + +
473C HIS* 4.2 2.7 - - - +
474C THR* 4.1 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C MET* 3.8 29.9 - - + +
14C PRO* 3.3 35.1 - - + +
16C SER 3.0 13.3 + - - +
17C PRO* 2.7 20.0 + - + +
19C THR* 1.3 70.7 - - - +
21C LEU* 1.3 60.9 + - + +
23C MET* 3.5 11.2 + - + +
24C LEU* 3.1 48.3 + - + +
39C GLU 5.5 0.2 - - - -
41C THR* 2.8 30.8 + - - -
42C TYR 4.7 6.3 - - - -
43C LEU* 3.9 7.9 - - + -
44C PRO* 6.4 0.2 - - + -
419C TYR* 4.4 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO 3.0 9.7 + - - +
18C GLU* 3.9 9.0 - - - +
20C HIS* 1.3 77.8 - - + +
22C ASP* 1.3 64.9 + - - +
24C LEU* 3.3 7.3 + - + +
25C ARG* 3.0 22.3 + - - +
43C LEU* 4.6 15.3 - - + -
44C PRO* 4.4 15.9 - - + -
46C ASN* 6.0 1.6 - - - +
47C ALA* 4.2 29.6 - - + -
48C SER 4.6 5.6 - - - +
49C LEU* 4.6 4.7 - - + -
51C PHE* 4.2 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU 3.3 16.5 + - - +
19C THR* 3.4 10.2 + - - +
20C HIS 3.4 0.2 - - - -
21C LEU* 1.3 79.2 - - - +
23C MET* 1.3 55.8 + - - +
25C ARG* 3.3 28.2 + - - +
26C HIS* 2.9 41.8 + - + +
472C LEU* 3.8 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C THR* 4.3 0.9 - - + -
9C MET* 3.7 26.0 - - + -
19C THR 2.9 12.2 + - - +
20C HIS* 3.8 12.6 - - - +
21C LEU 3.3 0.2 - - - -
22C ASP* 1.3 76.1 - - - +
24C LEU* 1.3 81.6 - - + +
25C ARG 3.1 0.3 + - - -
26C HIS* 3.2 1.6 + - - +
27C LEU* 2.8 57.6 + - + +
418C ALA* 4.0 11.4 - - + -
419C TYR* 3.3 34.8 - - + +
443C LEU* 3.7 21.9 - - + +
472C LEU* 3.6 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C THR* 5.2 3.8 - - + -
9C MET* 5.3 0.7 - - + -
20C HIS* 3.1 27.4 + - + +
21C LEU* 3.4 10.5 - - + +
23C MET* 1.3 102.3 - - + +
25C ARG* 1.3 56.8 + - - +
27C LEU* 4.3 1.3 - - - -
28C TYR* 3.0 47.3 + - + -
39C GLU 4.0 17.9 - - - +
40C LEU* 4.3 13.5 - - + -
41C THR 4.9 0.2 - - - +
43C LEU* 3.3 39.0 - - + -
51C PHE* 3.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 3.0 13.6 + - + +
22C ASP* 3.4 32.3 + - - +
24C LEU* 1.3 73.9 - - - +
26C HIS* 1.3 87.1 + - - +
29C GLN* 2.7 52.2 + - + +
51C PHE* 3.6 36.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASP* 2.9 33.4 + - + +
23C MET* 3.4 4.9 - - - +
25C ARG* 1.3 98.1 + - - +
27C LEU* 1.3 57.2 + - - +
29C GLN* 4.4 3.0 + - - +
443C LEU* 4.3 6.5 - - + -
467C PRO 4.9 7.0 + - - +
468C HIS* 2.8 42.3 + - - +
469C GLN 4.5 4.9 + - - -
470C ALA* 3.3 34.3 - - + +
472C LEU* 4.1 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C CYS* 3.3 19.0 - - + +
5C THR* 3.1 30.1 - - - +
6C GLY 4.6 2.5 - - - +
7C THR* 3.5 23.8 - - + -
23C MET* 2.8 45.9 + - + +
24C LEU 3.6 4.7 - - - +
26C HIS* 1.3 74.1 - - - +
28C TYR* 1.3 72.5 + - + +
417C GLY 5.2 0.4 - - - +
418C ALA* 4.6 7.6 - - + +
443C LEU* 5.8 4.9 - - + -
468C HIS* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C CYS* 3.6 20.9 - - - -
5C THR 4.3 3.6 - - - -
6C GLY* 3.5 8.1 - - - -
7C THR* 4.1 5.7 + - - +
24C LEU* 3.0 47.3 + - + +
27C LEU* 1.3 89.3 - - + +
29C GLN* 1.3 66.9 + - - +
30C GLY 3.0 0.5 + - - -
31C CYS* 2.8 22.6 + - - +
34C VAL* 3.6 24.2 - - + -
37C ASN 3.3 22.2 + - - -
38C LEU* 3.5 21.1 - - + -
39C GLU 4.0 3.5 + - - -
40C LEU* 4.7 1.1 - - + -
51C PHE* 3.3 19.6 - + + +
52C LEU* 3.9 21.1 - - + -
55C ILE* 3.8 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG* 2.7 39.3 + - + +
26C HIS* 4.4 2.9 - - - +
27C LEU 3.8 0.8 - - - -
28C TYR* 1.3 71.7 - - - +
30C GLY* 1.3 60.9 + - - +
31C CYS 3.3 2.3 + - - -
51C PHE* 3.5 30.7 + - + +
468C HIS* 3.8 14.9 - - - -
----------------------------------------------------------
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