Contacts of the helix formed by residues 35 - 44 (chain A) in PDB entry 1EIA
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 GLU 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 1.3 75.1 + - - +
36A ALA* 1.3 53.3 + - - +
38A GLN* 3.2 21.3 - - - +
39A ASN* 2.7 47.7 + - - +
141A ILE* 3.7 15.1 - - + +
145A ILE* 5.5 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 3.8 22.0 - - + -
30A ASN 5.6 0.4 - - - +
34A ASN* 2.7 21.8 + - - +
35A GLU* 1.3 73.4 - - - +
37A SER* 1.3 51.7 + - - +
39A ASN* 3.3 5.7 + - - +
40A LEU* 2.6 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.5 17.3 - - - -
26A THR* 3.8 9.2 - - - +
27A ILE* 3.7 10.2 - - - +
31A GLY* 2.3 43.5 + - - -
32A LEU* 3.5 9.6 - - - -
34A ASN 2.9 5.9 + - - -
36A ALA* 1.3 71.3 - - - +
38A GLN* 1.3 57.3 - - - +
40A LEU* 3.4 7.5 - - - +
41A PHE* 2.6 37.8 + - - +
137A MET* 4.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN 2.9 11.3 + - - +
35A GLU* 3.2 22.8 + - - +
37A SER* 1.3 77.9 - - - +
39A ASN* 1.3 72.8 + - - +
41A PHE* 3.2 3.3 + - - +
42A GLY* 2.9 19.6 + - - -
134A ILE* 4.6 14.8 - - + +
137A MET* 4.1 27.7 - - + +
138A SER* 4.0 22.9 + - - -
141A ILE* 3.5 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 2.7 29.1 + - - +
36A ALA* 3.7 5.2 - - - +
38A GLN* 1.3 86.6 - - - +
40A LEU* 1.3 58.3 + - - +
42A GLY* 3.0 3.6 + - - -
43A ILE* 2.8 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.6 24.7 - - + +
23A TRP* 4.0 14.8 - - + -
26A THR* 3.1 34.8 - - + +
36A ALA 2.6 20.8 + - - +
37A SER* 3.4 6.1 - - - +
39A ASN* 1.3 72.7 - - - +
41A PHE* 1.3 63.9 + - - +
43A ILE* 3.0 16.0 + - + +
44A LEU* 2.8 62.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
23A TRP* 3.9 22.6 - + + -
37A SER 2.6 21.0 + - - +
38A GLN 3.5 1.3 - - - +
40A LEU* 1.3 71.7 - - - +
42A GLY* 1.3 54.0 + - - +
44A LEU* 4.6 2.9 - - - -
45A SER* 2.4 70.1 + - - +
53A MET* 3.9 18.6 - - + -
56A PHE* 4.6 21.5 - + + -
57A LEU* 6.1 1.8 - - + -
130A ARG* 3.9 13.2 - - + -
133A ILE* 3.5 44.6 - - + -
134A ILE* 4.1 10.5 - - + -
137A MET* 3.2 28.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
38A GLN 2.9 14.6 + - - -
39A ASN* 3.4 4.7 - - - -
41A PHE* 1.3 81.7 - - - +
43A ILE* 1.3 62.2 + - - +
45A SER* 3.3 1.0 + - - -
46A VAL* 3.1 9.0 - - - +
130A ARG* 2.8 32.7 + - - -
134A ILE* 4.9 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 2.8 35.6 + - + +
40A LEU* 3.5 15.3 - - + +
42A GLY* 1.3 71.2 - - - +
44A LEU* 1.3 65.4 + - + +
46A VAL* 2.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 5.4 4.8 - - + +
19A GLY* 3.6 34.5 - - - +
22A THR* 6.0 0.2 - - - -
23A TRP* 4.4 12.1 - - + +
40A LEU* 2.8 55.1 + - + +
41A PHE 4.0 0.9 - - - +
43A ILE* 1.3 75.5 - - + +
45A SER* 1.3 53.3 + - - +
46A VAL* 2.7 23.7 + - - +
48A CYS* 3.8 7.6 - - - -
56A PHE* 3.8 32.3 - - + -
----------------------------------------------------------
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