Contacts of the helix formed by residues 37 - 52 (chain D) in PDB entry 1EFP
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 PRO 37 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C FAD 4.0 27.6 - - + -
10D LEU* 4.6 0.7 - - + -
11D ILE 5.8 0.2 - - - +
13D TYR* 3.9 35.2 - - + -
35D MET 3.1 8.2 - - - +
36D ASN* 1.3 93.5 - - - +
38D PHE* 1.3 60.5 + - + +
39D ASP 3.4 0.2 + - - -
40D GLU* 3.4 23.8 + - - +
41D ILE* 3.5 16.1 + - - +
124D ILE* 4.0 15.5 - - + -
182D LEU* 4.8 6.7 - - + +
187D PRO* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLN* 5.7 2.0 - - + -
244C THR* 4.1 22.4 - - + -
399C FAD 4.0 9.0 - - + -
36D ASN* 3.0 10.9 + - - +
37D PRO* 1.3 77.8 - - - +
39D ASP* 1.3 58.2 + - - +
41D ILE* 3.2 11.2 - - - +
42D ALA* 3.1 23.4 + - - +
120D GLY* 3.7 19.7 - - - -
121D LYS* 3.7 22.9 - - + +
122D GLN* 3.0 37.7 - - + -
124D ILE* 3.8 21.8 - - + -
180D ALA* 3.4 19.5 - - - +
181D ASP 4.4 0.4 - - - -
182D LEU* 3.6 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C AMP 2.6 32.7 + - - -
6D PRO 3.5 1.2 - - - +
7D VAL* 3.7 28.4 - - + +
8D LYS* 2.7 27.9 + - - +
35D MET* 4.0 7.4 - - + -
36D ASN* 2.7 37.2 + - - +
38D PHE* 1.3 68.2 - - - +
40D GLU* 1.3 62.8 + - - +
42D ALA* 3.1 8.9 + - - +
43D VAL* 2.9 26.9 + - - +
120D GLY 3.6 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D MET* 3.5 37.2 - - + +
36D ASN 3.3 5.8 + - - +
37D PRO* 3.6 16.6 - - - +
38D PHE 3.3 0.2 - - - -
39D ASP* 1.3 77.7 - - - +
41D ILE* 1.3 62.3 + - - +
43D VAL* 3.4 4.5 + - - +
44D GLU* 3.0 25.5 + - - +
74D THR* 5.6 3.8 - - - +
78D MET* 3.8 14.7 - - + +
187D PRO* 4.0 26.2 - - + +
188D ARG 5.5 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ARG* 5.9 2.0 - - - +
37D PRO 3.5 15.3 - - - +
38D PHE* 3.2 12.8 - - - +
40D GLU* 1.3 78.8 - - - +
42D ALA* 1.3 63.3 + - - +
44D GLU 3.3 0.2 + - - -
45D GLU* 3.0 19.6 + - - +
180D ALA* 3.7 20.9 - - + -
181D ASP 3.7 16.2 - - - +
182D LEU* 4.0 20.9 - - + +
184D LEU* 3.8 7.2 - - + -
185D ASN* 3.0 55.6 + - - +
187D PRO* 3.6 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 4.1 7.6 - - + -
6D PRO 5.1 0.4 - - - +
38D PHE 3.1 8.7 + - - +
39D ASP* 3.1 15.0 + - - +
41D ILE* 1.3 78.5 - - - +
43D VAL* 1.3 63.4 + - - +
45D GLU* 3.1 6.2 + - - +
46D ALA* 3.0 20.8 + - - +
118D ILE* 3.6 42.9 - - + +
119D ALA* 4.2 10.3 - - - +
120D GLY 4.5 0.2 - - - +
180D ALA* 4.3 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 3.7 22.6 - - + +
7D VAL* 3.7 14.1 - - + -
35D MET* 4.4 11.2 - - + -
39D ASP 2.9 19.9 + - - +
40D GLU* 3.7 6.7 - - - +
42D ALA* 1.3 73.1 - - - +
44D GLU* 1.3 66.8 + - - +
46D ALA* 2.8 20.5 + - + +
47D ILE* 2.9 32.6 + - + -
58D ILE* 5.9 1.8 - - + -
60D ALA* 5.9 0.7 - - + -
75D ALA* 4.4 15.0 - - + +
78D MET* 4.0 20.6 - - + -
80D ALA* 5.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLU 3.0 14.8 + - - +
41D ILE 3.5 5.2 - - - +
43D VAL* 1.3 80.2 - - - +
45D GLU* 1.3 61.2 + - - +
47D ILE* 3.4 5.3 + - - +
48D ARG* 2.9 49.5 + - - +
78D MET* 4.4 4.1 - - + +
185D ASN* 3.4 25.4 - - - +
186D GLU 3.8 10.5 - - - +
187D PRO* 3.9 6.1 - - + -
188D ARG* 2.9 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ILE 3.0 8.2 + - - +
42D ALA* 3.5 8.5 - - - +
43D VAL 3.1 0.2 - - - -
44D GLU* 1.3 72.9 - - - +
46D ALA* 1.3 66.7 + - - +
48D ARG* 3.0 17.1 + - - +
49D LEU* 2.9 35.2 + - + +
52D LYS* 5.8 0.5 + - - -
118D ILE* 4.4 16.6 - - + -
150D VAL* 4.0 25.0 + - + +
184D LEU* 3.5 39.2 - - + +
185D ASN* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D VAL* 4.0 14.1 - - + +
5D VAL* 3.6 30.5 - - + -
42D ALA 3.0 6.3 + - - +
43D VAL 2.8 14.7 + - - +
45D GLU* 1.3 71.8 - - - +
47D ILE* 1.3 62.5 + - - +
49D LEU* 3.0 18.9 + - - +
50D LYS 3.1 8.7 + - - -
55D ALA* 4.8 1.4 - - - +
58D ILE* 3.5 21.5 - - + +
118D ILE* 4.3 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D VAL* 2.9 33.6 + - + +
44D GLU* 3.6 9.0 - - - +
46D ALA* 1.3 76.5 - - + +
48D ARG* 1.3 58.2 + - - +
50D LYS* 2.9 26.6 + - - +
51D GLU* 3.0 28.1 + - + +
58D ILE* 3.6 17.0 - - + +
78D MET* 3.3 29.4 - - + +
79D GLY* 3.6 14.6 - - - +
80D ALA 4.6 0.4 - - - +
188D ARG* 3.0 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLU* 2.9 40.9 + - - +
45D GLU* 3.0 25.3 + - - +
47D ILE* 1.3 76.0 - - - +
49D LEU* 1.3 61.0 + - + +
51D GLU* 3.4 18.3 + - - +
52D LYS* 3.3 27.4 - - + +
184D LEU 5.6 0.4 + - - -
185D ASN* 3.9 18.2 - - - +
186D GLU* 3.3 34.8 + - - +
188D ARG* 4.8 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 6.0 0.7 - - - -
3D VAL* 4.5 8.1 - - + -
45D GLU* 2.9 31.8 + - + +
46D ALA 3.0 10.1 + - - +
48D ARG* 1.3 78.1 - - + +
50D LYS* 1.3 59.9 + - - +
52D LYS* 3.3 22.3 + - - +
54D GLN* 3.1 37.8 + - + +
55D ALA* 4.0 6.7 - - + -
116D LEU* 3.7 31.0 - - + -
118D ILE* 4.2 14.6 - - + -
150D VAL* 4.9 9.0 - - + +
152D ILE* 3.8 30.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
46D ALA 3.1 4.4 + - - -
47D ILE* 2.9 16.2 + - - +
49D LEU* 1.3 73.8 - - - +
51D GLU* 1.3 59.9 + - - +
52D LYS 2.9 10.3 + - - -
53D GLY* 3.0 13.3 + - - -
55D ALA* 3.3 26.1 - - + +
56D GLU 3.7 19.5 - - - +
58D ILE* 4.0 22.1 - - + +
79D GLY* 3.1 20.0 + - - -
81D ASP* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 3.0 25.1 + - + +
48D ARG* 3.8 15.5 - - - +
49D LEU 3.3 1.0 - - - -
50D LYS* 1.3 77.3 - - + +
52D LYS* 1.3 60.3 + - + +
53D GLY 3.6 0.9 - - - -
188D ARG* 2.8 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLU* 5.8 0.6 + - - -
48D ARG* 3.3 21.8 - - + +
49D LEU* 3.3 17.9 + - - +
50D LYS 3.0 1.6 - - - -
51D GLU* 1.3 80.8 - - + +
53D GLY* 1.3 65.0 + - - +
54D GLN* 3.3 35.1 + - + +
150D VAL 4.8 8.7 + - - -
151D GLU* 5.9 1.2 - - - +
152D ILE* 4.9 2.6 + - - +
----------------------------------------------------------
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