Contacts of the helix formed by residues 30 - 50 (chain A) in PDB entry 2PK2
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 ASP 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 1.3 74.9 - - - +
31A PRO* 1.3 70.0 - - - +
32A ASP* 4.1 10.1 - - - +
33A LYS* 3.3 25.8 - - + +
34A GLU* 2.6 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 2.8 44.0 - - - +
25A ARG* 3.0 28.0 + - + +
29A VAL 3.5 3.6 - - - +
30A ASP* 1.3 95.8 - - - +
32A ASP* 1.3 66.5 + - - +
34A GLU* 4.6 0.2 - - - +
35A LEU* 2.9 28.9 + - - +
230B THR* 5.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.1 11.3 - - + +
31A PRO* 1.3 85.7 - - - +
33A LYS* 1.3 56.0 + - - +
35A LEU* 3.1 26.4 - - + +
36A SER* 2.5 34.2 + - - -
247A LYS* 5.9 2.9 - - - +
232B GLU* 4.6 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.9 5.8 - - + -
30A ASP* 3.0 30.6 + - + +
32A ASP* 1.3 74.8 - - - +
34A GLU* 1.3 53.3 + - - +
35A LEU 3.0 1.1 - - - -
36A SER* 2.5 31.1 + - - -
37A TYR* 2.5 67.2 + - + +
40A GLN* 4.5 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 6.2 0.2 - - + -
22A SER* 2.8 33.8 + - - -
24A SER* 3.0 16.7 + - - -
25A ARG* 3.0 26.8 + - - +
29A VAL* 3.8 15.3 - - + +
30A ASP 2.6 12.7 + - - +
31A PRO 4.6 0.4 - - - +
33A LYS* 1.3 73.1 - - - +
35A LEU* 1.3 51.8 + - - +
37A TYR* 3.4 10.4 - - - +
38A ARG* 2.7 50.8 + - - +
70A TYR* 4.6 4.6 - - - +
75A PHE* 2.8 36.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO 2.9 20.0 + - - +
32A ASP* 3.1 35.9 - - + +
33A LYS 3.0 0.2 - - - -
34A GLU* 1.3 76.8 - - - +
36A SER* 1.3 53.1 + - - +
38A ARG* 3.8 11.6 - - - +
39A GLN* 2.7 52.1 + - - +
184A LEU 4.0 18.2 - - - +
185A THR* 5.4 1.6 - - - -
186A THR* 5.0 12.6 - - + -
244A ILE* 5.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP 2.5 12.7 + - - -
33A LYS* 2.5 47.5 + - - -
35A LEU* 1.3 71.3 - - - +
37A TYR* 1.3 58.7 + - - -
39A GLN* 3.8 8.2 + - - +
40A GLN* 2.6 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 4.6 16.4 - - + +
33A LYS* 2.5 51.1 + - + +
34A GLU* 3.4 12.6 - - - +
36A SER* 1.3 70.9 - - - +
38A ARG* 1.3 54.5 + - - +
40A GLN* 3.3 6.8 + - - +
41A ALA* 2.5 39.7 + - - +
75A PHE* 3.3 48.2 - + + -
76A THR* 5.3 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.1 20.8 - - - +
22A SER* 5.2 1.6 + - - -
34A GLU* 2.7 44.0 + - - +
35A LEU* 3.8 15.7 - - - +
36A SER 3.4 0.2 - - - -
37A TYR* 1.3 70.5 - - - +
39A GLN* 1.3 53.9 + - + +
41A ALA* 2.6 9.0 + - - +
42A ALA* 2.5 35.7 + - - +
66A MET* 4.0 5.4 + - - +
67A HIS* 3.6 59.5 + - + +
70A TYR* 4.7 12.0 + - - +
71A MET* 4.4 5.3 - - - +
75A PHE* 3.5 25.1 - - + -
183A HIS 4.9 0.2 - - - -
186A THR* 4.3 19.6 - - - +
189A LEU* 3.7 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 2.7 41.7 + - + +
36A SER* 3.8 10.0 + - - +
38A ARG* 1.3 74.4 - - + +
40A GLN* 1.3 60.8 + - - +
42A ALA* 3.0 7.9 + - - +
43A ASN* 2.8 25.6 + - - +
183A HIS* 3.4 26.5 + - - +
184A LEU* 3.0 45.4 - - + +
244A ILE* 5.7 2.3 - - - +
248A THR* 4.8 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 4.5 9.7 - - - +
36A SER* 2.6 43.6 + - - +
37A TYR* 3.4 7.1 - - - +
38A ARG 3.1 0.2 - - - -
39A GLN* 1.3 81.1 + - - +
41A ALA* 1.3 59.0 + - - +
43A ASN* 2.9 31.6 + - + +
44A LEU* 3.5 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR 2.5 19.6 + - - +
38A ARG 2.6 10.6 + - - +
40A GLN* 1.3 72.9 - - - +
42A ALA* 1.3 56.3 - - - -
44A LEU* 3.3 23.3 + - - +
45A LEU* 4.1 6.1 - - - +
66A MET* 3.9 21.6 - - + +
75A PHE* 4.1 6.3 - - + -
80A GLY* 4.1 26.9 - - - -
84A ALA* 4.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG 2.5 14.3 + - - +
39A GLN* 3.0 19.7 + - - +
41A ALA* 1.3 70.3 - - - +
43A ASN* 1.3 62.7 + - - +
44A LEU 3.1 0.7 - - - -
45A LEU* 3.2 16.7 + - - +
46A GLN* 3.3 10.6 + - - +
63A ILE* 3.4 35.8 - - + +
66A MET* 4.0 5.8 - - + +
183A HIS* 4.3 17.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN 2.8 10.6 + - - +
40A GLN* 2.9 20.0 + - + +
42A ALA* 1.3 73.6 - - - +
44A LEU* 1.3 54.2 + - - +
45A LEU 3.0 9.5 + - - -
46A GLN* 4.8 1.7 - - - +
47A ASP* 3.1 45.2 + - - +
48A MET 4.0 1.2 + - - -
111A CYS* 6.1 0.3 - - - -
254A ARG* 5.7 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLN 3.5 3.9 + - - +
41A ALA* 3.3 13.2 + - - +
42A ALA 3.1 1.0 - - - -
43A ASN* 1.3 75.7 - - - +
45A LEU* 1.3 58.4 + - - +
48A MET* 3.4 39.5 - - + +
80A GLY 3.5 7.4 - - - +
81A ASN* 2.8 50.0 - - - +
84A ALA* 2.9 25.6 - - + +
85A PRO* 4.7 1.3 - - + -
88A LEU* 4.4 0.3 - - - +
108A ALA* 5.7 0.2 - - - -
111A CYS* 4.2 17.9 - - + -
112A LEU* 4.4 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA 4.1 3.8 - - - +
42A ALA 3.2 13.0 - - - +
43A ASN 3.0 1.8 + - - -
44A LEU* 1.3 81.3 - - - +
46A GLN* 1.3 61.8 + - - +
47A ASP 3.7 0.2 - - - -
48A MET* 4.0 0.6 - - - +
49A GLY 3.4 11.4 + - - -
59A ILE* 3.2 54.0 - - + +
62A ALA* 3.3 17.7 - - + -
63A ILE* 3.2 36.6 - - + +
66A MET* 3.8 22.4 - - + -
84A ALA* 5.0 8.7 - - + +
87A ALA* 4.6 7.4 - - + -
88A LEU* 3.6 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 3.3 7.7 + - - +
43A ASN* 5.6 1.3 - - - +
45A LEU* 1.3 76.7 - - - +
47A ASP* 1.3 58.0 + - - +
48A MET 3.1 3.8 - - - -
49A GLY 4.0 0.2 - - - -
50A GLN* 2.4 62.7 + - - +
56A GLN* 3.0 36.3 + - - +
59A ILE* 3.3 25.8 - - + +
60A ASN* 3.6 5.2 - - - +
63A ILE* 4.9 0.2 - - + -
179A THR* 5.1 5.3 + - + -
183A HIS* 3.5 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN* 3.1 35.4 + - - +
46A GLN* 1.3 78.7 - - - +
48A MET* 1.3 59.1 + - - +
50A GLN* 3.0 34.0 + - - +
51A ARG* 3.9 16.8 + - - +
111A CYS* 4.1 5.0 - - - -
251A ARG* 5.9 1.4 + - - -
254A ARG* 5.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN 4.0 1.4 + - - +
44A LEU* 3.4 50.0 - - - +
45A LEU 4.0 0.2 - - - +
46A GLN 3.1 0.8 - - - +
47A ASP* 1.3 78.9 - - - +
49A GLY* 1.3 56.8 + - - +
50A GLN 3.0 4.5 - - - -
51A ARG* 2.9 28.2 + - - +
52A LEU* 3.6 9.9 - - + +
85A PRO* 4.2 26.9 - - + -
88A LEU* 3.7 22.2 - - + -
104A VAL 4.3 9.9 - - - +
107A VAL* 3.4 23.2 - - + +
108A ALA* 4.4 8.7 - - - +
111A CYS* 3.3 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU 3.4 10.6 + - - -
48A MET* 1.3 74.0 - - - +
50A GLN* 1.4 58.8 + - - +
51A ARG 3.0 6.3 + - - -
52A LEU* 3.2 25.1 + - - +
53A ASN 3.5 7.6 + - - -
54A VAL* 3.6 10.1 + - - +
59A ILE* 3.3 31.8 - - - +
88A LEU* 3.9 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 2.4 56.7 + - - +
47A ASP* 3.0 32.5 + - - +
48A MET 3.0 0.4 - - - -
49A GLY* 1.4 76.6 - - - +
51A ARG* 1.4 59.1 + - - +
53A ASN* 4.2 7.6 + - - +
56A GLN* 5.8 0.9 - - - +
59A ILE* 4.8 0.9 - - - -
----------------------------------------------------------
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