Contacts of the helix formed by residues 35 - 44 (chain D) in PDB entry 3P05
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LYS* 2.9 54.0 - - - +
33D SER* 2.6 32.6 + - - -
34D PRO* 1.3 69.0 - - - +
36D VAL* 1.3 67.0 + - - +
37D ILE 3.0 3.2 + - - -
38D PRO* 3.3 11.7 - - - +
39D MET* 3.2 20.8 + - - +
173D ARG* 4.0 7.1 - - - +
233D IOD 3.6 9.5 - - - +
57E ASN 3.9 9.8 - - - +
58E THR* 3.6 9.1 - - - +
59E VAL 3.7 15.3 - - - +
60E GLY* 3.3 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TRP* 4.4 22.8 - - + -
26D VAL* 4.7 8.3 - - + +
27D VAL* 4.5 8.1 - - + -
30D LYS* 3.9 22.2 - - + -
31D ALA 3.4 24.2 - - - +
32D PHE* 4.6 17.0 - - + -
33D SER 3.1 15.4 + - - +
35D GLU* 1.3 79.6 - - - +
37D ILE* 1.3 59.5 + - + +
39D MET* 3.5 7.1 + - - +
40D PHE* 2.8 27.1 + - + +
138D LEU* 5.1 7.6 - - + -
142D VAL* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PRO* 3.2 8.9 + - + +
35D GLU 3.0 3.6 - - - -
36D VAL* 1.3 75.3 - - + +
38D PRO* 1.4 73.6 - - + +
40D PHE* 3.2 9.6 + - - +
41D SER* 3.0 21.0 + - - +
135D ILE* 4.1 29.2 - - + -
138D LEU* 4.0 16.4 - - + -
139D ASN* 3.0 46.7 - - - +
142D VAL* 4.1 19.1 - - + -
176D GLN* 4.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PRO 3.5 8.1 - - - +
35D GLU 3.3 9.4 - - - +
37D ILE* 1.4 96.6 - - + +
39D MET* 1.3 53.7 + - - +
41D SER* 3.3 8.3 + - - +
42D ALA* 2.9 29.5 + - - +
173D ARG* 4.0 9.4 - - - +
54E THR* 5.1 3.4 - - + +
57E ASN* 3.4 34.8 - - + +
58E THR* 4.1 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D CYS* 5.0 4.3 - - - -
23D TRP* 5.2 1.6 - - + -
26D VAL* 3.9 26.9 - - + -
30D LYS* 3.5 19.1 - - - +
35D GLU 3.2 14.0 + - - +
36D VAL* 3.6 7.9 - - - +
37D ILE 3.2 0.2 - - - -
38D PRO* 1.3 75.4 - - - +
40D PHE* 1.3 67.2 + - - +
42D ALA* 3.3 2.8 + - - +
43D LEU* 2.8 48.3 + - + +
20E LEU* 4.4 18.4 - - - +
24E VAL* 3.1 38.8 - - + -
58E THR* 3.6 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TRP* 3.7 36.9 - + + -
36D VAL 2.8 21.5 + - - +
37D ILE 3.5 4.5 - - - +
39D MET* 1.3 72.3 - - - +
41D SER* 1.3 66.3 + - - +
43D LEU* 3.2 2.9 + - - +
44D SER* 3.0 29.3 + - - -
52D LEU* 3.6 27.8 - - + -
55D MET* 3.9 24.0 - - + -
56D LEU* 5.0 6.1 - - + -
131D LYS* 3.9 22.4 - - + -
134D ILE* 3.7 30.1 - - + -
135D ILE* 4.0 21.3 - - + -
138D LEU* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 3.0 13.1 + - - +
38D PRO* 3.6 11.2 - - - +
40D PHE* 1.3 77.4 - - - +
42D ALA* 1.3 63.3 + - - +
44D SER* 3.2 19.4 + - - -
45D GLU* 3.3 20.8 + - - +
131D LYS* 3.5 9.0 + - - +
135D ILE* 3.6 24.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
38D PRO 2.9 17.0 + - - +
39D MET* 3.9 2.2 - - - +
41D SER* 1.3 77.5 - - - +
43D LEU* 1.3 63.0 + - - +
44D SER 3.4 0.5 + - - -
45D GLU* 4.0 17.3 + - - +
15E ILE* 5.0 13.3 - - + +
17E PRO* 5.3 4.3 - - - +
20E LEU* 3.4 30.7 - - + +
54E THR* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D THR* 3.7 25.9 - - + +
22D CYS* 4.3 6.3 - - - -
23D TRP* 3.7 43.5 - - + +
39D MET* 2.8 38.7 + - + +
40D PHE 3.2 4.2 + - - +
42D ALA* 1.3 81.2 - - - +
44D SER* 1.3 57.1 + - - +
45D GLU 3.6 2.0 + - - -
55D MET* 4.1 14.3 - - + +
17E PRO* 4.0 34.6 - - + +
20E LEU* 4.9 8.7 - - + -
21E CYS* 4.5 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PHE* 3.0 20.7 + - - -
41D SER* 3.2 0.5 + - - -
42D ALA 3.2 0.8 - - - -
43D LEU* 1.3 78.4 - - - +
45D GLU* 1.3 65.0 + - - +
47D ALA* 3.1 21.1 + - - +
52D LEU* 4.0 23.8 - - - -
55D MET* 4.0 12.1 - - - -
131D LYS* 2.9 36.7 + - - +
----------------------------------------------------------
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