Contacts of the helix formed by residues 16 - 32 (chain A) in PDB entry 2Q24
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 16 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 1.3 63.1 + - - +
18A ASP* 3.7 6.7 - - - +
19A LYS* 3.5 39.8 - - - +
20A ILE* 2.9 36.8 + - - +
44A ALA* 4.8 0.7 - - - +
46A VAL* 5.5 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 1.3 77.6 - - - +
18A ASP* 1.3 66.2 + - - +
20A ILE* 3.3 9.6 + - - +
21A LEU* 3.0 51.6 + - + +
54A ASN* 6.3 1.1 - - + -
55A PHE* 3.8 32.6 - - + -
64A ALA* 4.2 6.3 + - - +
68A ASN* 4.1 2.0 - - - +
120B ASP* 4.4 3.4 + - - -
123B GLY* 3.6 28.2 + - - -
124B ASP* 2.8 32.5 + - - -
127B GLN* 3.5 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN 3.3 6.4 - - - +
17A ARG* 1.3 82.6 + - - +
19A LYS* 1.3 53.8 + - + +
21A LEU* 3.7 4.1 - - - +
22A ALA* 2.8 37.0 + - - +
68A ASN* 3.1 28.3 + - - +
72A ARG* 4.1 18.7 - - - +
124B ASP* 4.8 0.9 - - - +
127B GLN* 5.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 3.4 29.5 + - - +
18A ASP* 1.3 76.7 - - + +
20A ILE* 1.3 64.7 + - - +
22A ALA* 3.9 4.6 - - - +
23A ALA* 3.0 24.6 + - - +
26A ARG* 5.3 0.5 + - - -
43A GLU 5.6 1.3 - - - +
44A ALA* 3.3 35.5 + - + +
45A GLY* 4.7 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN 2.9 22.2 + - - +
17A ARG* 3.7 6.1 - - - +
19A LYS* 1.3 75.5 - - - +
21A LEU* 1.3 59.4 + - - +
23A ALA* 3.3 4.0 + - - +
24A ALA* 2.8 25.8 + - - +
40A ILE* 3.6 5.8 - - + +
44A ALA* 3.6 20.4 - - + -
46A VAL* 4.0 29.6 - - + -
50A THR* 4.9 1.8 - - + -
51A LEU* 3.5 35.2 - - + -
54A ASN* 4.7 10.3 - - + +
55A PHE* 3.8 26.0 - - + -
61A LEU* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.0 60.4 + - + +
18A ASP 4.1 0.4 - - - +
20A ILE* 1.3 74.9 - - - +
22A ALA* 1.3 63.6 + - - +
24A ALA* 3.3 3.5 + - - +
25A VAL* 3.0 29.1 + - - +
55A PHE* 3.7 23.3 - - + -
61A LEU* 3.8 18.2 - - + -
64A ALA* 3.7 8.3 - - + +
65A ALA* 3.7 23.9 - - + +
68A ASN* 3.6 36.1 - - + +
72A ARG* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP 2.8 22.5 + - - +
19A LYS* 3.9 5.6 - - - +
21A LEU* 1.3 69.4 - - - +
23A ALA* 1.3 65.0 + - - +
25A VAL* 3.3 10.5 + - - +
26A ARG* 3.2 31.1 + - - +
68A ASN* 4.9 1.8 + - - -
72A ARG* 5.6 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS 3.0 19.6 + - - +
20A ILE 3.3 4.5 + - - +
22A ALA* 1.3 74.9 - - - +
24A ALA* 1.3 57.5 - - - +
26A ARG* 3.2 17.3 + - - +
27A VAL* 3.0 33.3 + - - +
40A ILE* 3.7 27.1 - - + +
43A GLU* 4.0 20.9 - - + +
44A ALA 4.4 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE 2.8 18.1 + - - +
21A LEU* 3.3 12.1 + - - +
23A ALA* 1.3 69.2 - - - +
25A VAL* 1.3 66.4 + - - +
28A PHE* 2.9 36.6 + - + +
40A ILE* 3.7 14.3 - - + +
61A LEU* 4.0 26.2 - - + -
65A ALA* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU 3.0 16.7 + - - +
22A ALA* 3.7 9.0 - - - +
23A ALA 3.3 0.2 - - - -
24A ALA* 1.3 73.0 - - - +
26A ARG* 1.3 56.9 + - - +
28A PHE* 4.2 0.3 - - - +
29A SER* 2.6 44.2 + - - +
65A ALA* 4.0 17.5 - - + +
69A GLU* 3.6 37.7 - - + +
72A ARG* 5.6 1.6 - - - +
103A ALA* 4.1 17.7 - - + -
107A MSE 4.1 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS 5.3 0.4 + - - -
22A ALA* 3.2 14.2 + - - +
23A ALA* 3.2 31.9 + - - +
25A VAL* 1.3 81.1 - - - +
27A VAL* 1.3 59.7 + - + +
29A SER* 3.4 6.0 + - - -
30A GLU* 3.0 35.7 + - + +
39A ARG* 6.1 1.8 - - - +
43A GLU* 3.4 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 3.0 13.4 + - - +
26A ARG* 1.3 73.9 - - + +
28A PHE* 1.3 57.2 + - - +
31A GLU* 2.7 47.5 + - - +
35A ALA* 3.8 17.5 - - + -
36A HIS 4.3 3.8 - - - +
39A ARG* 3.6 42.8 - - + +
40A ILE* 3.5 31.4 - - + -
43A GLU* 3.6 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 2.9 31.6 + - + +
25A VAL* 4.2 1.8 - - - +
27A VAL* 1.3 75.8 - - - +
29A SER* 1.3 59.2 + - - +
32A GLY* 2.8 45.5 + - - -
33A LEU 4.0 13.2 - - - -
35A ALA* 3.7 16.4 - - + -
37A LEU* 4.2 7.4 - - + -
40A ILE* 3.9 9.4 - - + -
58A ARG* 4.2 10.5 - - + -
61A LEU* 3.8 36.3 - - + -
62A ILE* 3.5 37.7 - - + -
65A ALA* 5.4 2.0 - - + -
106A GLY 4.3 3.4 - - - +
107A MSE 4.4 12.8 - - + -
110A ALA* 4.2 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 2.6 31.6 + - - +
26A ARG* 3.6 6.3 - - - -
27A VAL 3.2 0.2 - - - -
28A PHE* 1.3 79.6 - - - +
30A GLU* 1.3 61.3 + - - +
32A GLY* 4.5 1.4 + - - -
103A ALA* 4.2 1.4 + - - -
106A GLY* 3.3 41.2 - - - +
107A MSE 3.6 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 3.0 20.9 + - + +
27A VAL* 3.9 2.0 - - - +
29A SER* 1.3 77.5 - - - +
31A GLU* 1.3 64.6 + - + +
39A ARG* 2.5 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 2.7 29.2 + - - +
30A GLU* 1.3 79.0 - - + +
32A GLY* 1.3 60.1 + - - +
33A LEU 4.1 0.2 + - - -
34A ASP* 4.2 11.1 + - - +
35A ALA* 3.4 11.1 + - - -
36A HIS* 3.1 36.0 + - - +
39A ARG* 2.6 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 2.8 39.2 + - - -
29A SER 4.5 1.8 + - - -
30A GLU 3.7 1.2 - - - -
31A GLU* 1.3 70.5 - - - +
33A LEU* 1.3 66.0 + - - -
34A ASP 3.1 2.9 - - - -
35A ALA* 3.1 12.3 + - - +
109A ASP* 4.9 14.1 - - - -
110A ALA* 4.6 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