Contacts of the helix formed by residues 48 - 62 (chain D) in PDB entry 2P1N
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 THR 48 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 3.7 11.3 + - - -
12D ASP* 4.7 8.5 + - - +
46D ASN 4.0 3.0 + - - -
47D VAL* 1.3 81.3 - - - +
49D SER* 1.3 54.2 + - - +
50D LYS* 2.4 58.5 - - + +
51D ILE* 2.9 17.0 - - + +
52D LEU* 2.8 30.1 + - - +
100D GLU* 3.9 19.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D SER* 2.5 32.5 + - - -
12D ASP* 3.2 11.2 + - - -
14D GLU* 3.1 30.9 + - - +
16D PHE* 3.8 16.4 - - - -
48D THR* 1.3 69.5 - - - +
50D LYS* 1.3 69.5 + - - +
51D ILE 2.8 0.7 + - - -
52D LEU* 2.9 1.1 + - - -
53D ALA* 2.7 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D THR* 2.4 25.1 - - + +
49D SER* 1.3 76.5 - - - +
51D ILE* 1.3 71.4 - - + +
53D ALA* 3.2 19.6 - - - +
54D LYS* 3.4 10.9 + - - +
94D ASP* 5.1 2.2 + - - -
97D THR* 3.5 29.4 + - - +
100D GLU* 5.2 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 3.4 22.2 - - + -
48D THR* 2.9 12.3 - - + +
49D SER 2.8 0.8 + - - -
50D LYS* 1.3 101.2 - - + +
52D LEU* 1.3 68.7 + - - +
53D ALA 3.1 1.5 + - - -
54D LYS* 3.2 7.7 + - + +
55D VAL* 2.9 25.7 + - + +
97D THR* 4.4 13.2 - - + +
100D GLU* 3.7 38.8 - - + +
101D LEU* 4.2 14.4 - - + +
104D ALA* 3.5 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 3.8 32.1 - - + +
10D SER* 4.4 13.5 - - - +
16D PHE* 3.6 28.7 - - + -
44D LEU* 4.0 18.6 - - + -
47D VAL* 3.4 12.3 - - + +
48D THR 2.8 20.3 + - - +
49D SER* 3.6 6.1 - - - +
51D ILE* 1.3 77.6 - - - +
53D ALA* 1.3 53.8 + - - +
55D VAL* 3.5 13.6 + - + +
56D ILE* 2.7 57.4 + - + +
108D LEU* 5.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D PHE* 4.0 21.0 - - + -
49D SER 2.7 15.6 + - - +
50D LYS* 3.2 13.5 - - - +
51D ILE 3.1 0.2 - - - -
52D LEU* 1.3 70.9 - - - +
54D LYS* 1.4 52.1 + - - +
56D ILE* 3.1 7.1 + - - +
57D GLU* 2.9 33.2 + - - +
60D LYS* 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LYS 3.4 8.9 + - - +
51D ILE* 3.2 12.1 + - + +
53D ALA* 1.4 74.3 - - - +
55D VAL* 1.3 66.6 + - - +
57D GLU* 3.0 28.6 + - - +
58D TYR* 3.0 14.9 + - - +
89D ASP 5.6 0.2 + - - -
90D PHE* 3.5 40.7 + - + +
92D LYS 4.9 1.0 + - - -
93D ILE* 3.0 41.6 - - - +
97D THR* 5.2 9.4 - - + -
101D LEU* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE* 2.9 23.5 + - + +
52D LEU* 3.7 13.7 - - + +
54D LYS* 1.3 73.3 - - - +
56D ILE* 1.3 55.8 + - - +
58D TYR* 4.1 5.3 - - - +
59D CYS* 3.0 32.0 + - - +
90D PHE* 5.7 0.2 - - - -
101D LEU* 3.9 13.2 - - + +
104D ALA* 4.1 18.2 - - + -
108D LEU* 4.0 21.8 - - + -
110D ILE* 4.1 17.0 - - + -
113D LEU* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 3.9 9.9 - - + -
16D PHE* 3.9 21.1 - - + -
18D VAL* 3.5 36.3 - - + -
22D VAL* 4.5 3.6 - - + -
52D LEU* 2.7 50.2 + - + +
53D ALA* 3.1 8.7 + - - +
55D VAL* 1.3 71.0 - - - +
57D GLU* 1.3 57.5 + - - +
59D CYS* 3.6 4.6 - - - +
60D LYS* 2.7 63.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ALA 2.9 12.3 + - - +
54D LYS* 3.3 32.8 + - - +
56D ILE* 1.3 79.8 - - - +
58D TYR* 1.3 61.7 + - - +
60D LYS* 3.2 20.4 + - - +
61D ARG* 3.2 32.6 + - + +
89D ASP* 5.5 3.3 - - - +
90D PHE* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS 3.0 9.4 + - - +
55D VAL* 4.1 3.1 - - - +
57D GLU* 1.3 73.2 - - - +
59D CYS* 1.3 81.0 + - - +
61D ARG* 3.0 15.3 + - - -
62D HIS* 3.2 48.1 + + - -
87D ASP* 3.8 10.9 + - - -
90D PHE* 3.8 34.5 - + + -
110D ILE* 4.6 4.3 - - + -
112D ASN* 2.6 54.0 + - - +
113D LEU* 3.5 39.7 - - + -
116D LEU* 4.2 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D VAL* 3.7 31.2 - - + +
25D GLU* 3.7 35.7 - - + +
55D VAL* 3.0 26.5 + - - +
56D ILE* 4.6 0.4 - - - -
58D TYR* 1.3 88.1 - - - +
60D LYS* 1.4 62.7 + - - +
62D HIS* 3.6 17.7 - - - +
110D ILE* 4.0 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D VAL* 5.9 0.4 - - + -
19D GLU* 5.7 3.8 - - - +
22D VAL* 3.9 22.8 - - + +
53D ALA 5.6 0.2 + - - -
56D ILE* 2.7 43.1 + - + +
57D GLU* 3.4 21.7 - - - +
58D TYR 3.0 0.2 - - - -
59D CYS* 1.4 75.1 - - - +
61D ARG* 1.3 64.2 + - - +
62D HIS 3.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 3.2 21.4 + - + +
58D TYR* 3.0 11.2 + - - +
60D LYS* 1.3 77.6 - - - +
62D HIS* 1.3 73.1 + - + +
86D TRP* 2.6 38.8 + - - +
87D ASP* 3.9 9.5 + - - +
89D ASP* 4.3 11.3 + - - +
90D PHE* 4.5 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLU* 4.3 14.6 - - - +
58D TYR* 3.2 45.5 + + + +
59D CYS* 3.6 14.0 - - - +
60D LYS 3.6 5.9 - - - +
61D ARG* 1.3 90.1 - - + +
87D ASP* 3.0 40.1 + - - -
112D ASN* 3.9 20.4 - - + +
----------------------------------------------------------
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