Contacts of the helix formed by residues 34 - 53 (chain A) in PDB entry 5NJ8
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 ASN 34 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 1.3 74.6 - - + +
36A SER* 3.4 8.7 - - - +
37A LYS* 3.8 18.7 + - + +
38A ARG* 3.6 18.9 + - - +
7E G 3.7 31.7 + - - +
8E C 5.6 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 1.3 92.0 - - + +
36A SER* 1.3 61.5 + - - +
37A LYS 3.3 0.2 - - - -
38A ARG* 2.7 37.3 - - + +
39A HIS* 3.1 10.6 + - - +
1F G 5.3 6.1 - - - +
2F G 4.1 13.2 + - - +
3F T 4.6 7.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
34A ASN* 3.4 5.5 - - - +
35A PRO* 1.3 79.7 - - - +
37A LYS* 1.3 66.1 + - - +
39A HIS* 3.1 16.0 + - - +
40A ARG* 3.0 40.7 + - - +
7E G 4.4 7.0 + - - -
8E C 3.6 28.5 + - - -
9E A 5.4 1.7 + - - -
3F T 5.4 3.3 - - - +
5F G 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.8 22.1 + - + +
35A PRO 3.3 0.6 - - - -
36A SER* 1.3 78.5 - - - +
38A ARG* 1.3 59.5 + - - +
40A ARG* 3.5 24.0 + - - +
41A ASP* 2.9 53.8 + - - +
6E C 4.2 19.1 + - - +
7E G 5.2 7.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
34A ASN 3.6 7.1 + - - +
35A PRO* 2.7 38.0 - - + +
37A LYS* 1.3 77.9 - - + +
39A HIS* 1.3 70.2 + - - +
41A ASP* 3.1 6.0 + - - -
42A ARG* 2.9 44.0 + - + +
1F G 3.5 16.0 + - - -
2F G 2.5 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO 3.1 16.6 + - - +
36A SER* 3.1 19.1 - - - +
38A ARG* 1.3 79.7 - - - +
40A ARG* 1.3 70.6 + - + +
42A ARG* 3.6 7.2 - - - +
43A LEU* 3.0 45.2 + - + +
129B LEU* 5.3 3.6 - - + +
3F T 3.6 49.8 + - + +
4F T 3.3 37.4 + - + +
5F G 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 3.0 32.0 + - - +
37A LYS* 4.1 16.0 - - - +
39A HIS* 1.3 88.8 - - + +
41A ASP* 1.3 58.2 + - - +
43A LEU* 3.3 7.7 + - - +
44A ASN* 2.9 43.1 + - - +
5E A 3.7 19.4 + - - +
6E C 2.4 65.1 + - - +
7E G 4.1 20.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 2.9 43.3 + - + +
38A ARG* 3.1 8.0 + - - +
40A ARG* 1.3 76.5 - - - +
42A ARG* 1.3 60.2 + - - +
44A ASN* 2.7 26.6 + - - +
45A THR* 3.0 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 2.9 39.3 + - + +
39A HIS* 3.6 6.8 - - - +
41A ASP* 1.3 74.7 + - - +
43A LEU* 1.3 63.2 + - - +
45A THR* 3.2 26.0 - - + +
46A GLU* 3.6 16.6 - - - +
129B LEU* 3.9 15.9 - - + +
133B ARG* 4.2 16.7 - - - +
2F G 2.9 48.1 + - - -
3F T 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 3.0 45.0 + - + +
40A ARG* 3.5 7.9 - - - +
42A ARG* 1.3 80.1 - - - +
44A ASN* 1.3 68.7 + - - +
46A GLU* 3.9 7.8 + - - +
47A LEU* 3.4 26.8 + - + +
105B MET* 6.0 5.8 - - + -
128B LYS* 5.5 7.4 - - + -
129B LEU* 4.9 17.9 - - + +
132B LEU* 4.2 23.1 - - + +
4F T 5.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 2.9 30.6 + - - +
41A ASP* 2.7 18.9 + - - +
43A LEU* 1.3 79.1 - - - +
45A THR* 1.3 58.3 + - - +
46A GLU 3.0 2.2 - - - -
47A LEU* 2.7 33.1 + - + +
48A ASP* 2.9 11.7 + - - +
66A LYS* 3.4 33.9 + - - +
5E A 3.6 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.0 11.9 + - - +
42A ARG* 3.2 31.0 - - + +
44A ASN* 1.3 75.0 - - - +
46A GLU* 1.3 65.4 + - + +
48A ASP* 3.3 9.4 + - - +
49A ARG* 2.9 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG 3.6 16.5 - - - +
43A LEU 3.9 6.4 + - - +
44A ASN 3.0 0.8 - - - -
45A THR* 1.3 80.8 - - + +
47A LEU* 1.3 60.5 + - - +
49A ARG* 4.5 15.3 - - - +
50A LEU* 2.9 32.4 + - - +
129B LEU* 2.9 31.9 - - - +
132B LEU* 3.3 22.5 - - + +
133B ARG* 2.6 49.5 + - + +
136B VAL* 3.8 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.4 26.9 - - + +
44A ASN* 2.7 19.3 + - - +
46A GLU* 1.3 73.2 - - - +
48A ASP* 1.3 54.7 + - - +
50A LEU* 3.8 5.8 - - + +
51A ALA* 2.9 30.8 + - - +
66A LYS* 4.4 37.9 - - + +
69A VAL* 3.7 14.2 - - + +
70A LEU* 4.8 16.2 - - + -
105B MET* 5.0 11.7 - - + -
132B LEU* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN 2.9 10.7 + - - +
45A THR* 3.6 12.8 - - - +
46A GLU 3.2 0.2 - - - -
47A LEU* 1.3 73.9 - - - +
49A ARG* 1.3 68.6 + - + +
51A ALA* 3.3 6.0 + - - +
52A SER* 2.9 25.8 + - - -
227C LEU* 3.7 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 2.9 44.0 + - - +
46A GLU* 3.8 14.6 - - - +
48A ASP* 1.3 77.9 + - + +
50A LEU* 1.3 64.4 + - - +
52A SER* 2.9 15.8 + - - -
53A LEU* 2.9 23.3 + - + +
136B VAL* 4.6 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU 2.9 21.7 + - - +
47A LEU* 3.8 5.8 - - - +
49A ARG* 1.3 72.2 - - - +
51A ALA* 1.3 63.7 + - - +
53A LEU* 2.9 19.0 + - - +
54A LEU* 3.4 7.1 + - + +
69A VAL* 4.3 10.8 - - + -
70A LEU* 4.4 11.7 - - + -
73A SER* 3.3 26.2 - - - +
112B LEU* 4.4 18.2 - - + -
132B LEU* 5.1 6.1 - - + +
135B ALA* 4.8 10.5 - - + +
136B VAL* 4.0 14.9 - - + +
139B MET* 3.2 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU 2.9 19.8 + - - +
48A ASP* 3.5 7.4 - - - +
50A LEU* 1.3 75.3 - - - +
52A SER* 1.3 59.1 + - - +
54A LEU* 2.8 43.5 + - + +
61A ILE* 3.6 21.1 - - + +
64A LEU* 4.7 2.7 - - + -
69A VAL* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 2.9 18.7 + - - -
49A ARG* 2.9 12.1 + - - -
51A ALA* 1.3 75.6 - - - +
53A LEU* 1.3 64.5 + - - +
54A LEU 3.3 5.1 + - - +
61A ILE* 4.1 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 2.9 21.4 + - + +
50A LEU* 2.9 13.9 + - - +
52A SER* 1.3 81.0 - - - +
54A LEU* 1.3 65.1 + - - +
55A PRO* 3.8 1.4 - - - +
76A TYR* 6.1 0.2 - - - -
136B VAL* 4.1 13.7 - - + +
139B MET* 3.6 28.0 - - + +
140B LYS* 3.5 42.0 - - + +
143B ARG 6.0 2.9 - - - -
----------------------------------------------------------
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