Contacts of the helix formed by residues 24 - 37 (chain C) in PDB entry 3SDL
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 SER 24 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.8 2.1 - - - +
22C SER 3.8 4.2 + - - -
23C MET* 1.3 76.6 - - - +
25C VAL* 1.3 66.1 + - - +
26C SER* 3.0 21.9 + - - -
27C GLU* 3.0 19.1 + - - +
28C LEU* 3.0 20.1 + - - +
56C ASP 5.0 3.3 + - - -
57C ARG 5.4 2.9 + - - -
59C PRO* 4.4 6.1 - - - -
60C LEU* 4.0 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C SER* 1.3 71.8 + - - +
26C SER* 1.3 64.8 + - - +
28C LEU* 3.0 15.5 + - - +
29C LYS* 3.1 26.5 + - + +
45C LEU* 4.7 8.1 - - + -
54C LEU* 4.3 14.1 - - + -
55C GLN 3.4 23.6 - - - +
56C ASP* 3.2 39.9 + - - +
58C VAL 3.5 13.4 + - - +
60C LEU* 3.6 24.5 - - + +
63C GLN* 4.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C SER* 3.0 16.0 + - - -
25C VAL* 1.3 79.4 - - - +
27C GLU* 1.3 68.8 + - - +
29C LYS* 3.7 8.8 + - - +
30C ALA* 3.3 20.4 + - - +
56C ASP* 4.4 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.9 7.4 - - + -
22C SER 5.6 5.2 - - - +
24C SER* 3.0 20.7 + - - +
26C SER* 1.3 89.3 + - - +
28C LEU* 1.3 55.3 + - - +
30C ALA* 3.1 16.8 + - - +
31C GLN* 2.8 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 3.7 32.8 - - + -
7C VAL* 4.8 3.1 - - + -
17C VAL* 3.8 22.2 - - + -
19C LEU* 4.1 10.2 - - + +
24C SER 3.0 11.0 + - - +
25C VAL* 3.0 11.1 + - - +
27C GLU* 1.3 75.9 - - - +
29C LYS* 1.3 58.0 + - - +
31C GLN* 3.1 5.6 + - - +
32C ILE* 2.8 43.4 + - + +
45C LEU* 3.6 25.4 - - + -
54C LEU* 4.1 19.5 - - + -
60C LEU* 4.1 11.7 - - + -
71C VAL* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL* 3.1 14.1 + - + +
26C SER* 3.9 10.1 - - - +
28C LEU* 1.3 76.2 - - - +
30C ALA* 1.3 59.5 + - - +
32C ILE 3.3 0.5 + - - -
33C THR* 2.9 18.6 + - - -
40C ALA* 4.0 25.9 + - + +
41C PHE* 6.0 0.2 - - - +
43C GLN* 2.8 68.2 + - - +
44C ARG* 5.0 3.0 - - - +
45C LEU* 3.7 25.8 - - + +
56C ASP* 3.3 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C SER 3.3 12.0 + - - +
27C GLU* 3.1 21.9 + - - +
29C LYS* 1.3 77.6 - - - +
31C GLN* 1.3 61.1 + - - +
33C THR* 3.4 9.0 + - - -
34C GLN* 3.2 26.6 + - - +
40C ALA* 5.1 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 3.3 30.2 - - + +
18C SER* 3.5 40.3 + - - +
19C LEU* 5.4 1.8 - - + -
27C GLU 2.8 14.4 + - - +
28C LEU* 3.3 11.2 - - - +
30C ALA* 1.3 73.4 - - - +
32C ILE* 1.3 65.4 + - - +
34C GLN* 3.1 10.8 + - - +
35C LYS* 3.0 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 4.0 31.9 - - + -
15C PHE* 4.2 6.5 - - + -
17C VAL* 4.3 5.2 - - + -
28C LEU* 2.8 25.0 + - + +
29C LYS 3.7 1.1 - - - +
31C GLN* 1.3 75.4 - - - +
33C THR* 1.3 63.6 + - - +
35C LYS* 3.1 6.8 + - - -
36C ILE* 2.9 50.4 + - + +
38C VAL* 4.6 2.7 - - + -
43C GLN* 3.3 32.5 - - - +
45C LEU* 3.8 22.7 - - + -
73C LEU* 3.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS 2.9 17.2 + - - -
30C ALA* 3.5 13.0 - - - +
31C GLN 3.2 0.2 - - - -
32C ILE* 1.3 76.2 - - - +
34C GLN* 1.3 61.4 + - + +
37C GLY* 2.8 31.0 + - - -
38C VAL 2.6 31.0 + - - +
39C HIS* 4.7 5.8 - - - +
40C ALA* 3.4 11.3 + - - +
43C GLN* 3.1 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA 3.2 11.6 + - - +
31C GLN* 3.1 13.3 + - - +
33C THR* 1.3 82.7 - - + +
35C LYS* 1.3 64.7 + - + +
37C GLY 4.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 4.3 22.0 - - + -
16C GLN* 2.9 35.0 + - - +
17C VAL* 4.9 6.4 - - + +
18C SER 5.8 0.2 - - - +
31C GLN* 3.0 23.2 + - + +
32C ILE* 3.6 6.7 - - - +
34C GLN* 1.3 79.9 - - - +
36C ILE* 1.3 69.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 2.9 37.0 + - - +
9C MET* 3.9 11.9 - - + -
13C ASN* 5.8 2.0 - - - +
15C PHE* 3.6 49.4 - - + -
32C ILE* 2.9 32.0 + - + +
35C LYS* 1.3 79.3 - - + +
37C GLY* 1.3 58.5 + - - +
38C VAL* 3.7 22.4 - - + +
73C LEU* 3.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 4.0 8.7 + - - -
33C THR* 2.8 23.0 + - - -
34C GLN 4.5 0.8 + - - -
35C LYS 3.8 0.4 - - - -
36C ILE* 1.3 79.9 - - - +
38C VAL* 1.3 62.4 + - - +
39C HIS* 3.5 12.5 + - - -
----------------------------------------------------------
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