Contacts of the helix formed by residues 17 - 30 (chain A) in PDB entry 1PR9
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 LYS 17 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY 3.5 6.1 - - - +
16A GLY* 1.3 79.8 - - - +
18A GLY* 1.3 66.8 + - - +
19A ILE 3.6 0.2 + - - -
20A GLY 3.5 4.7 + - - -
21A ARG* 3.1 19.2 + - - +
40A THR* 4.5 3.8 + - - +
43A ASP* 2.5 38.6 + - - +
185A SER* 4.1 17.9 - - - +
245A NAP 2.9 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 1.3 73.8 - - - +
19A ILE* 1.3 57.9 + - - -
21A ARG* 3.1 6.4 + - - +
22A GLY* 3.0 24.9 + - - -
184A THR* 3.6 19.5 - - - -
185A SER* 5.2 0.6 + - - -
212A VAL* 4.4 8.3 - - - +
245A NAP 3.5 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY* 1.3 68.1 - - - -
20A GLY* 1.3 57.5 + - - +
22A GLY* 3.3 1.0 + - - -
23A THR* 2.7 45.3 + - - +
83A ASN* 3.5 19.1 - - - +
134A VAL* 5.0 1.1 - - + -
179A PRO* 4.7 3.4 - - + -
182A VAL* 4.2 16.4 - - + -
184A THR* 4.1 3.6 - - + +
212A VAL* 4.2 21.8 - - + -
215A VAL* 3.8 47.1 - - + -
216A VAL* 4.2 2.9 - - + +
219A ILE* 4.2 6.3 - - + -
245A NAP 3.0 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.9 9.7 - - - +
14A GLY 3.4 8.3 - - - -
15A ALA* 3.9 7.2 - - - -
17A LYS 3.5 2.0 + - - -
18A GLY 3.3 0.8 - - - -
19A ILE* 1.3 79.4 - - - +
21A ARG* 1.3 60.3 + - - +
23A THR* 3.2 7.2 + - - -
24A VAL* 3.0 26.7 + - - +
81A VAL* 6.4 0.2 - - - -
83A ASN* 3.3 28.1 + - - -
245A NAP 4.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 3.3 18.2 + - - +
16A GLY 3.0 22.5 + - - -
17A LYS* 3.1 18.8 + - - +
18A GLY 3.5 9.0 - - - +
20A GLY* 1.3 74.5 - - - +
22A GLY* 1.3 61.1 + - - +
24A VAL* 3.3 4.5 + - - +
25A GLN* 3.0 37.5 + - - +
43A ASP* 3.2 22.6 + - - +
46A SER* 3.2 21.4 + - - -
47A LEU* 3.5 20.9 - - + +
50A GLU* 2.5 40.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 3.0 13.6 + - - -
19A ILE 3.3 3.3 + - - -
20A GLY 3.3 0.2 - - - -
21A ARG* 1.3 75.7 - - - +
23A THR* 1.3 62.7 + - - +
25A GLN* 3.5 11.2 + - - +
26A ALA* 3.2 22.9 + - - +
212A VAL* 4.1 14.6 - - - -
216A VAL* 3.8 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.4 13.0 - - + -
19A ILE* 2.7 23.3 + - - +
20A GLY* 3.5 7.9 - - - -
22A GLY* 1.3 74.8 - - - +
24A VAL* 1.3 64.8 + - - +
26A ALA* 3.5 1.6 + - - +
27A LEU* 3.0 41.6 + - + +
81A VAL* 4.5 7.6 - - + +
216A VAL* 3.5 23.7 - - + +
219A ILE* 3.8 35.0 - - + +
220A LEU* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.9 10.3 - - + -
15A ALA* 3.7 26.0 - - + -
20A GLY 3.0 14.2 + - - +
21A ARG 3.3 7.4 + - - +
23A THR* 1.3 76.8 - - - +
25A GLN* 1.3 57.4 + - - +
27A LEU* 3.2 4.6 + - - +
28A HIS* 2.7 28.6 + - - +
34A VAL* 3.8 32.2 - - + +
36A ALA* 4.4 1.1 - - + -
47A LEU* 4.0 24.9 - - + -
51A CYS* 4.7 2.7 - - - -
54A ILE* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.0 26.0 + - - +
22A GLY* 3.9 9.9 - - - +
23A THR 3.3 0.2 - - - -
24A VAL* 1.3 75.8 - - - +
26A ALA* 1.3 56.8 + - - +
28A HIS* 3.2 2.6 + - - +
29A ALA* 2.8 30.7 + - - +
47A LEU* 4.0 7.3 - - + +
50A GLU* 2.9 37.4 + - - +
51A CYS* 3.9 23.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 3.2 14.8 + - - +
23A THR 3.8 2.9 - - - +
25A GLN* 1.3 76.9 - - - +
27A LEU* 1.3 62.0 + - - +
29A ALA* 3.2 6.6 + - - +
30A THR* 2.8 31.0 + - + +
216A VAL* 3.7 24.2 - - + -
220A LEU* 4.5 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.7 31.2 - - + -
10A VAL* 3.8 41.7 - - + -
12A VAL* 4.1 9.6 - - + -
23A THR* 3.0 36.0 + - + +
24A VAL* 3.7 2.7 - - - +
26A ALA* 1.3 77.3 - - - +
28A HIS* 1.3 66.1 + - - +
30A THR* 2.9 20.7 + - - +
32A ALA* 3.3 20.7 + - + -
34A VAL* 3.9 13.5 - - + -
81A VAL* 5.2 0.2 - - + -
220A LEU* 3.7 12.8 - - + -
223A LEU* 4.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL 2.7 21.7 + - - +
25A GLN 3.5 5.1 + - - +
27A LEU* 1.3 72.1 - - - +
29A ALA* 1.3 66.9 + - - +
31A GLY* 3.2 11.8 + - - -
32A ALA 4.5 13.1 + - - +
34A VAL* 4.2 3.3 - - + +
50A GLU 5.0 1.3 + - - -
51A CYS* 3.6 38.6 - - + +
52A PRO* 2.7 33.9 + - + -
53A GLY* 5.2 0.9 - - - -
54A ILE* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN 2.8 17.2 + - - +
26A ALA* 3.7 7.2 - - - +
27A LEU 3.1 0.2 - - - -
28A HIS* 1.3 81.0 + - - +
30A THR* 1.3 63.5 + - + +
31A GLY* 3.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.0 23.9 - - + +
6A ALA* 3.4 20.4 + - - +
26A ALA* 2.8 20.0 - - + +
27A LEU* 2.9 14.8 + - + +
29A ALA* 1.3 80.6 - - + +
31A GLY* 1.3 57.2 + - - +
32A ALA* 4.0 2.3 + - - +
220A LEU* 5.5 9.2 - - + -
----------------------------------------------------------
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