Contacts of the helix formed by residues 4 - 18 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 4.4 20.6 - - - +
49C GLN* 4.2 17.4 + - - -
2D LYS* 3.6 30.1 + - - +
3D PHE* 1.3 74.8 - - - +
5D ARG* 1.3 65.9 + - - +
6D SER* 3.1 10.0 + - - +
7D GLY* 3.1 16.4 + - - +
8D ARG* 3.1 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 5 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 3.2 15.9 + - - -
3D PHE 3.5 3.7 + - - -
4D ARG* 1.3 72.1 - - - +
6D SER* 1.3 62.2 + - - +
8D ARG* 3.3 35.0 + - - +
9D LEU* 3.2 32.1 + - - +
42D GLU* 3.2 24.0 + - - -
43D ASP* 3.9 11.1 + - - +
46D ILE* 2.8 37.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 5.2 3.3 - - - -
9C LEU* 3.2 22.3 - - - +
46C ILE* 3.8 28.1 - - - +
4D ARG* 3.2 8.6 - - - +
5D ARG* 1.3 74.6 - - - +
7D GLY* 1.3 66.1 + - - +
8D ARG 3.1 1.8 - - - -
9D LEU* 3.2 10.1 + - - +
10D VAL* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 4.4 2.5 - - - +
50C THR* 3.3 33.3 - - - +
3D PHE* 4.2 8.3 - - - -
4D ARG* 3.1 12.0 + - - +
6D SER* 1.3 78.0 - - - +
8D ARG* 1.3 57.6 + - - +
10D VAL* 3.1 2.0 + - - -
11D ASP* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D PHE* 4.1 24.1 + - + +
4D ARG 3.1 10.7 + - - +
5D ARG* 3.5 30.1 - - - +
6D SER 3.1 1.0 - - - -
7D GLY* 1.3 77.8 - - - +
9D LEU* 1.3 57.3 + - - +
11D ASP* 3.9 2.8 - - - +
12D LEU* 2.9 35.2 + - + +
33D TYR* 3.5 43.7 - - + -
35D SER* 3.0 28.6 + - - -
39D SER* 4.1 16.7 + - - -
40D ILE* 3.9 10.5 - - - +
43D ASP* 2.6 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 3.7 37.0 - - - +
9C LEU* 4.6 12.8 - - + -
10C VAL* 3.9 17.3 - - + -
5D ARG* 3.2 28.1 + - - +
6D SER* 3.2 11.2 + - - +
8D ARG* 1.3 76.6 - - - +
10D VAL* 1.3 59.9 + - + +
12D LEU* 3.7 3.1 - - - +
13D THR* 2.8 30.2 + - - -
43D ASP* 4.0 29.3 + - + +
46D ILE* 4.7 4.7 - - + -
47D ILE* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.4 18.8 - - + -
13C THR* 3.5 27.3 - - - +
46C ILE* 4.6 5.6 - - + -
47C ILE* 3.8 23.8 - - + -
50C THR* 4.0 13.5 - - + -
51C PHE* 3.7 30.7 - - + -
6D SER 3.2 12.3 + - - +
7D GLY 3.1 7.2 + - - +
9D LEU* 1.3 76.1 - - - +
11D ASP* 1.3 64.5 + - - +
13D THR* 3.3 5.5 + - - -
14D ASN* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C THR* 4.2 6.7 - - + -
54C GLN* 2.9 36.8 - - - +
56C ILE* 4.4 6.4 - - - +
3D PHE* 4.2 6.7 - - + -
7D GLY 2.8 16.5 + - - +
8D ARG 3.9 2.0 - - - +
10D VAL* 1.3 76.0 - - - +
12D LEU* 1.3 59.7 + - - +
14D ASN* 3.2 8.4 + - - +
15D TYR* 2.8 27.4 + - - +
32D ARG* 2.9 25.9 + - - -
33D TYR* 2.4 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ARG* 2.9 18.6 + - + +
9D LEU* 3.7 1.6 - - - +
11D ASP* 1.3 75.5 - - - +
13D THR* 1.3 58.9 + - - +
15D TYR* 3.1 3.4 + - - +
16D LEU* 2.9 36.3 + - + +
29D PHE* 3.7 41.5 - - + -
33D TYR* 3.1 17.2 + - + -
40D ILE* 4.6 7.0 - - + -
43D ASP* 3.5 38.4 - - + +
44D LEU* 3.9 22.4 - - + -
47D ILE* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.7 42.5 - - + +
13C THR* 3.9 13.0 - - + -
14C ASN 4.4 0.2 - - - +
9D LEU 2.8 20.3 + - - -
10D VAL* 3.4 5.4 - - - -
11D ASP 3.2 0.2 - - - -
12D LEU* 1.3 76.3 - - - +
14D ASN* 1.3 65.5 + - - +
16D LEU* 3.4 5.2 + - - +
17D LEU* 3.0 46.6 + - + +
47D ILE* 3.7 14.7 - - - +
51D PHE* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C THR* 4.4 2.4 - - + +
17C LEU* 3.3 39.7 - - + +
51C PHE* 5.1 0.4 - - + -
56C ILE* 3.7 39.6 - - + +
10D VAL 3.1 11.2 + - - +
11D ASP* 3.6 8.1 + - - +
13D THR* 1.3 75.8 - - - +
15D TYR* 1.3 64.4 + - - +
17D LEU* 3.4 1.3 + - - -
18D THR* 2.8 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASP* 2.8 17.7 + - - +
12D LEU* 3.1 8.0 + - - +
14D ASN* 1.3 82.4 - - - +
16D LEU* 1.3 62.7 + - - +
18D THR* 3.2 3.8 + - - -
19D HIS* 2.7 69.8 + + - +
22D GLU* 4.8 5.0 + - - -
24D ILE* 3.8 23.2 - - + +
28D PHE* 3.3 36.8 - + - -
29D PHE* 3.8 19.7 - + + -
32D ARG* 3.9 27.6 - - - +
33D TYR* 4.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 2.9 24.9 + - + +
13D THR* 3.9 3.1 - - - +
15D TYR* 1.3 76.3 - - - +
17D LEU* 1.3 62.6 + - - +
19D HIS 3.0 17.5 + - - +
24D ILE* 4.0 24.7 - - + -
29D PHE* 4.3 5.8 - - + -
44D LEU* 4.0 12.3 - - + -
47D ILE* 4.0 21.1 - - + -
51D PHE* 4.6 7.0 - - + -
59D LEU* 4.0 40.4 - - + -
69D VAL* 4.3 13.5 - - + -
70D LYS 5.4 0.2 - - - -
71D TYR* 3.3 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASN* 3.3 39.9 - - + +
17C LEU* 3.9 17.3 - - + -
18C THR* 5.7 2.0 - - + -
13D THR* 3.0 37.8 + - + +
14D ASN* 3.9 4.0 - - - +
16D LEU* 1.3 75.4 - - - +
18D THR* 1.3 63.4 + - + +
19D HIS 3.7 0.2 + - - -
20D PRO* 3.7 11.3 - - - +
51D PHE* 3.8 20.6 - - + -
56D ILE* 3.9 2.2 - - + -
71D TYR* 3.8 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 5.8 0.9 - - + -
151C TYR* 6.0 1.3 - - - +
14D ASN* 2.8 42.2 + - - +
15D TYR* 3.2 8.0 + - - -
17D LEU* 1.3 78.8 - - + +
19D HIS* 1.3 79.2 + - - +
20D PRO* 3.3 9.6 - - - +
153D ASN* 5.9 0.3 + - - -
----------------------------------------------------------
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