Contacts of the helix formed by residues 4 - 19 (chain C) in PDB entry 1P4A
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 ARG 4 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LYS 4.3 0.6 + - - -
3C PHE* 1.3 75.3 - - - +
5C ARG* 1.3 65.4 + - - +
6C SER* 3.2 12.2 + - - +
7C GLY* 3.3 6.6 + - - +
8C ARG* 3.0 20.7 + - - +
46D ILE* 3.4 38.0 - - - +
49D GLN* 3.4 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 5 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE 3.9 1.0 + - - -
4C ARG* 1.3 71.7 - - - +
6C SER* 1.3 56.2 + - - +
8C ARG* 3.2 27.5 + - - +
9C LEU* 2.9 48.0 + - - +
39C SER* 3.8 3.0 + - - +
42C GLU* 3.5 24.4 + - - +
43C ASP* 2.3 47.7 + - - +
46C ILE* 4.0 16.8 - - - +
6D SER* 5.2 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 6 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 4.3 13.1 + - - +
5C ARG* 1.3 74.6 - - - +
7C GLY* 1.3 66.7 + - - +
9C LEU* 3.2 8.1 + - - +
10C VAL* 3.1 24.9 + - - +
5D ARG* 3.2 25.8 + - - -
9D LEU* 3.7 12.6 - - - +
46D ILE* 3.6 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 4.0 11.7 - - - -
4C ARG* 3.3 12.7 + - - +
6C SER* 1.3 78.3 - - - +
8C ARG* 1.3 57.0 + - - +
10C VAL* 3.1 1.3 + - - -
11C ASP* 2.8 31.9 + - - +
46D ILE* 4.0 4.1 - - - +
50D THR* 3.4 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LYS* 5.4 3.4 - - - +
3C PHE* 4.0 23.6 + - + -
4C ARG 3.0 12.7 + - - +
5C ARG* 3.3 32.0 - - - +
6C SER 3.1 0.2 - - - -
7C GLY* 1.3 75.8 - - - +
9C LEU* 1.3 57.2 + - - +
11C ASP* 3.9 1.1 - - - +
12C LEU* 2.8 38.0 + - + +
33C TYR* 3.4 51.8 + - + -
35C SER* 3.1 24.7 + - - -
39C SER* 3.9 19.4 + - - -
40C ILE* 4.3 2.6 - - - +
43C ASP* 2.6 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 2.9 30.5 + - - +
6C SER* 3.2 8.0 + - - +
8C ARG* 1.3 75.4 - - - +
10C VAL* 1.3 62.2 + - + +
12C LEU* 3.9 4.3 - - - +
13C THR* 2.8 31.4 + - - -
43C ASP* 3.9 39.2 + - + +
46C ILE* 4.4 7.4 - - + -
47C ILE* 4.1 13.5 - - + +
6D SER* 3.2 42.2 - - - +
9D LEU* 4.6 13.2 - - + -
10D VAL* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER 3.1 17.3 + - - +
7C GLY 3.1 6.5 + - - +
9C LEU* 1.3 76.6 - - - +
11C ASP* 1.3 64.9 + - - +
13C THR* 3.4 3.4 + - - -
14C ASN* 3.1 21.7 + - - +
9D LEU* 3.9 22.2 - - + +
10D VAL* 6.2 0.2 - - - +
13D THR* 3.7 23.4 - - - +
46D ILE* 4.4 6.5 - - + -
47D ILE* 4.0 16.2 - - + -
50D THR* 3.8 19.5 - - + -
51D PHE* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 4.2 3.6 - - + -
7C GLY 2.8 17.1 + - - +
10C VAL* 1.3 77.6 - - - +
12C LEU* 1.3 50.6 - - - +
14C ASN* 3.2 7.3 + - - +
15C TYR* 2.8 32.9 + - - +
32C ARG* 2.7 28.4 + - - -
33C TYR* 2.5 34.7 + - + +
50D THR* 4.0 11.2 - - + +
54D GLN* 3.0 35.9 - - - +
56D ILE* 4.4 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG 2.8 18.6 + - - +
9C LEU* 3.9 1.1 - - - +
11C ASP* 1.3 76.9 - - - +
13C THR* 1.3 56.3 + - - +
15C TYR* 3.2 3.6 + - - +
16C LEU* 2.8 38.3 + - + +
29C PHE* 3.5 44.2 - - + -
33C TYR* 3.2 20.7 + - + +
40C ILE* 4.5 6.7 - - + -
43C ASP* 3.6 37.2 - - + +
44C LEU* 3.9 18.8 - - + -
47C ILE* 3.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 2.8 20.7 + - - -
10C VAL 3.6 4.5 - - - -
11C ASP 3.3 0.2 - - - -
12C LEU* 1.3 77.7 - - - +
14C ASN* 1.3 65.6 + - - +
16C LEU* 3.4 4.6 + - - +
17C LEU* 3.0 47.3 + - + +
47C ILE* 3.7 9.2 - - - +
51C PHE* 4.1 10.5 - - + -
10D VAL* 3.5 47.0 - - + +
13D THR* 3.9 12.1 - - + -
14D ASN 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL 3.1 12.9 + - - +
11C ASP* 3.6 9.3 + - - +
13C THR* 1.3 78.4 - - - +
15C TYR* 1.3 68.1 + - - +
17C LEU* 3.3 1.8 + - - -
18C THR* 3.0 44.5 + - - +
32C ARG* 5.9 1.8 - - - +
13D THR* 4.4 2.4 - - + +
17D LEU* 3.3 39.5 - - + +
51D PHE* 5.1 0.9 - - + -
56D ILE* 3.6 38.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
11C ASP* 2.8 24.5 + - - +
12C LEU* 3.2 4.2 + - - +
14C ASN* 1.3 78.6 - - - +
16C LEU* 1.3 62.6 + - - +
18C THR* 3.8 3.6 - - - -
19C HIS* 2.8 66.4 + + - +
22C GLU* 4.8 4.0 + - - -
24C ILE* 3.8 23.7 - - + +
28C PHE* 3.4 36.5 - + - -
29C PHE* 3.7 28.3 - + + -
32C ARG* 4.1 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 2.8 27.9 + - + +
13C THR* 3.9 3.4 - - - +
15C TYR* 1.3 72.1 - - - +
17C LEU* 1.3 62.9 + - - +
19C HIS* 3.1 23.9 + - - +
24C ILE* 4.2 16.2 - - + -
29C PHE* 4.6 4.3 - - + -
44C LEU* 3.9 23.8 - - + -
47C ILE* 4.1 17.5 - - + -
51C PHE* 4.8 4.9 - - + -
59C LEU* 4.1 21.8 - - + -
69C VAL* 4.0 26.9 - - + -
71C TYR* 3.3 36.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C THR* 3.0 38.5 + - + +
14C ASN* 3.7 4.5 - - - +
16C LEU* 1.3 78.7 - - - +
18C THR* 1.3 61.3 + - + +
19C HIS 3.2 0.6 + - - -
20C PRO* 3.5 12.5 - - - +
51C PHE* 3.8 17.3 - - + -
56C ILE* 4.1 2.0 - - + -
71C TYR* 3.8 32.6 - - + +
14D ASN* 3.3 33.2 - - + +
17D LEU* 3.9 22.9 - - + -
18D THR* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASN* 3.0 40.6 + - - +
15C TYR* 3.3 2.6 + - - -
16C LEU 3.3 0.2 - - - -
17C LEU* 1.3 79.9 - - + +
19C HIS* 1.3 84.9 + - - +
20C PRO* 3.4 7.0 - - - +
17D LEU* 5.7 2.2 - - + -
151D TYR* 5.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR* 2.8 66.8 + + - +
16C LEU 3.1 9.8 + - - +
18C THR* 1.3 98.0 + - - +
20C PRO* 1.3 65.9 - - - +
21C HIS 3.7 0.3 + - - -
22C GLU* 3.6 44.4 + - - +
24C ILE* 4.3 12.3 - - + +
71C TYR* 4.9 3.1 + - - +
153C ASN* 6.1 1.1 - - - -
117D LYS* 6.0 4.2 + - - -
----------------------------------------------------------
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