Contacts of the helix formed by residues 38 - 59 (chain A) in PDB entry 2E9D
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 ILE 38 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 3.9 2.3 - - - +
37A LYS* 1.3 78.8 - - + +
39A ARG* 1.4 69.2 + - - +
40A ALA* 3.2 13.9 - - + +
41A PHE* 2.8 27.5 + - + +
42A GLY 3.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 4.5 16.2 - - - +
32A ALA* 4.6 5.5 - - - +
37A LYS 4.2 0.4 + - - -
38A ILE* 1.4 70.3 - - - +
40A ALA* 1.3 65.2 + - - +
42A GLY* 2.8 13.9 + - - +
43A HIS* 3.0 31.5 + - + +
81A GLU* 5.7 3.0 + - - -
701A B76 3.8 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 2.9 15.0 + - + +
39A ARG* 1.3 78.2 - - - +
41A PHE* 1.3 61.7 + - - +
43A HIS* 3.3 12.3 + - - +
44A LYS* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 3.4 35.2 - + - -
32A ALA* 5.0 0.4 - - + -
35A GLN* 4.2 7.4 - - - -
37A LYS* 3.1 61.9 - - + -
38A ILE* 2.8 20.9 + - + +
40A ALA* 1.3 75.5 - - - +
42A GLY* 1.3 62.6 + - - +
44A LYS* 3.4 11.0 + - + +
45A ALA* 3.1 18.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN* 3.9 29.7 + - - -
31A TRP* 4.1 9.6 - - - -
32A ALA* 4.0 9.0 - - - +
38A ILE 3.5 3.8 + - - -
39A ARG 2.8 8.5 + - - -
41A PHE* 1.3 78.2 - - - +
43A HIS* 1.3 54.9 + - - -
45A ALA* 3.0 4.5 + - - +
46A GLY* 2.7 32.4 + - - -
222A PRO* 4.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN* 4.3 8.5 + - + +
29A GLY 5.5 0.4 - - - -
39A ARG* 3.0 36.4 + - + +
40A ALA* 3.3 10.7 + - - +
42A GLY* 1.3 75.1 - - - +
44A LYS* 1.3 57.9 + - - +
46A GLY* 3.0 1.2 + - - +
47A ALA* 2.8 33.0 + - - +
701A B76 2.6 112.0 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 3.1 12.6 + - - +
41A PHE* 3.4 16.2 - - + +
42A GLY 3.1 0.4 - - - -
43A HIS* 1.3 78.9 - - - +
45A ALA* 1.3 57.0 + - - +
47A ALA* 3.5 7.0 + - + +
48A LYS* 3.1 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 3.4 40.6 - - + -
41A PHE* 3.1 3.9 + - + +
42A GLY 3.0 6.3 + - - +
44A LYS* 1.3 79.1 - - - +
46A GLY* 1.3 59.2 + - - +
48A LYS* 3.4 13.5 + - + +
49A SER* 2.9 26.3 + - - -
222A PRO* 3.6 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN* 3.7 19.3 - - - -
42A GLY 2.7 14.0 + - - -
43A HIS 3.0 3.8 + - - -
45A ALA* 1.3 75.7 - - - +
47A ALA* 1.3 52.9 + - - +
49A SER* 2.9 2.4 + - - -
50A VAL* 2.8 32.2 + - - +
221A TRP* 3.0 24.9 + - - -
222A PRO* 4.3 0.6 - - - +
701A B76 4.5 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A HIS 2.8 18.3 + - - +
44A LYS* 3.9 7.9 - - + +
46A GLY* 1.3 68.0 - - - -
48A LYS* 1.3 67.2 + - - +
50A VAL* 3.1 22.8 + - - +
51A ARG* 3.2 15.9 + - - +
701A B76 4.5 18.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 3.1 19.6 + - + +
45A ALA* 3.4 11.9 - - + +
47A ALA* 1.3 79.3 - - - +
49A SER* 1.3 62.4 + - - +
51A ARG* 3.5 8.9 + - - +
52A ARG* 3.4 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 2.9 15.0 + - - -
46A GLY 2.9 9.8 + - - -
48A LYS* 1.3 77.0 - - - +
50A VAL* 1.3 62.4 + - - +
52A ARG* 3.5 17.7 + - - +
53A ALA* 3.1 23.6 + - - +
221A TRP* 2.8 41.5 + - - -
222A PRO* 3.9 2.9 - - - -
224A PHE 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET* 4.0 15.5 - - + -
46A GLY 2.8 19.9 + - - +
47A ALA* 3.1 15.0 + - - +
49A SER* 1.3 78.9 - - - +
51A ARG* 1.3 60.8 + - + +
53A ALA* 3.4 2.9 + - - +
54A VAL* 3.1 22.7 + - - +
67A LEU* 3.7 18.1 - - + +
221A TRP* 3.9 15.5 - - - +
701A B76 4.7 9.6 - - + -
702A B76 3.3 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.2 10.0 + - - +
48A LYS* 3.8 10.8 - - - +
49A SER 3.3 0.2 - - - -
50A VAL* 1.3 75.6 - - + +
52A ARG* 1.3 67.2 + - - +
54A VAL* 3.5 6.0 + - - +
55A SER* 3.0 28.8 + - - +
96A GLU* 5.8 2.0 + - - -
702A B76 3.8 71.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 3.4 23.8 + - - +
49A SER* 3.2 24.6 + - - +
51A ARG* 1.3 81.5 - - - +
53A ALA* 1.3 60.1 + - - +
55A SER* 3.6 6.3 - - - -
56A PHE* 3.2 22.3 + - - +
222A PRO 3.3 20.0 + - - -
223A ASP* 4.3 1.0 - - - +
224A PHE 2.5 34.5 + - - +
225A ASP* 3.3 35.2 + - - +
226A GLU* 3.1 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.9 2.7 - - + -
49A SER 3.1 17.3 + - - +
50A VAL* 3.7 4.7 - - - +
51A ARG 3.2 0.2 - - - -
52A ARG* 1.3 74.1 - - - +
54A VAL* 1.3 70.4 + - - +
56A PHE* 3.3 2.7 + - - +
57A ALA* 3.1 13.9 + - - +
65A LEU* 4.1 7.9 - - + -
67A LEU* 5.3 2.7 - - + -
221A TRP* 3.9 22.2 - - + -
224A PHE* 5.3 4.0 - - + +
229A PHE* 3.5 31.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.1 17.4 + - + +
51A ARG 3.7 6.7 - - - +
53A ALA* 1.3 76.5 - - - +
55A SER* 1.3 55.9 + - - +
57A ALA* 2.5 34.5 + - - +
58A ALA* 3.0 5.1 + - + -
65A LEU* 3.7 18.8 - - + +
67A LEU* 5.0 0.4 - - + -
105A VAL* 4.7 6.5 - - + -
137A LEU* 4.0 15.0 - - + -
139A LEU* 3.6 21.5 - - + -
702A B76 3.2 55.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 3.0 17.3 + - - +
52A ARG* 3.6 8.2 - - - -
54A VAL* 1.3 79.8 - - - +
56A PHE* 1.3 64.0 + - - +
58A ALA* 3.2 2.2 + - - +
59A ASN* 2.8 41.4 + - - +
226A GLU* 4.8 5.8 - - - -
702A B76 3.0 43.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG 3.2 10.9 + - - +
53A ALA 3.5 8.5 - - - +
54A VAL 2.9 2.0 + - - -
55A SER* 1.3 78.6 - - - +
57A ALA* 1.3 64.0 + - - +
59A ASN* 4.4 2.7 - - - +
60A ASN* 2.8 61.9 + - + +
62A ILE* 4.6 0.9 - - + -
226A GLU* 3.5 31.4 - - + -
229A PHE* 3.7 31.0 - + + -
230A GLU* 3.1 50.7 - - + -
233A LEU* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA 3.1 10.7 + - - +
54A VAL 2.5 22.8 + - - +
56A PHE* 1.3 69.7 - - - +
58A ALA* 1.3 65.8 + - - +
60A ASN 3.2 4.0 + - - -
62A ILE* 3.1 46.7 + - + +
65A LEU* 4.0 11.2 - - + -
137A LEU* 3.3 31.9 - - + -
229A PHE* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL 3.0 8.1 + - - +
55A SER* 3.6 9.9 - - - +
57A ALA* 1.3 74.5 - - - +
59A ASN* 1.3 61.6 + - - +
60A ASN 2.6 15.8 + - - -
61A GLY* 3.1 11.3 + - - -
62A ILE 5.1 0.7 - - - -
103A HIS 5.4 7.4 - - - +
105A VAL* 5.4 2.9 - - + -
137A LEU* 4.0 24.0 - - + +
702A B76 5.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 2.8 32.9 + - - +
56A PHE* 4.2 2.2 - - - +
58A ALA* 1.3 77.5 - - - +
60A ASN* 1.3 72.5 + - - +
61A GLY 3.7 0.4 - - - -
226A GLU* 5.9 0.4 + - - -
702A B76 3.7 27.6 + - - +
----------------------------------------------------------
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