Contacts of the helix formed by residues 24 - 37 (chain C) in PDB entry 3IFS
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 LEU 24 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B GLY* 4.3 23.3 - - - -
20C GLU 3.5 19.1 - - - +
21C ILE 2.8 17.0 + - - +
23C TYR* 1.3 76.0 - - + +
25C ARG* 1.3 62.6 + - - +
26C ASP 3.4 2.2 - - - -
27C ALA* 3.3 11.9 + - + +
28C VAL* 2.9 25.2 + - + +
246C LEU* 3.8 3.4 - - - -
256C VAL* 3.9 36.1 - - + +
259C ASN* 5.7 4.3 - - + -
260C ALA* 6.5 0.4 - - + -
411C LEU* 4.3 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR* 3.2 16.4 + - + +
23C TYR 3.5 0.6 - - - -
24C LEU* 1.3 77.7 - - - +
26C ASP* 1.3 87.7 + - - +
28C VAL* 3.4 2.1 + - - +
29C LYS* 3.0 51.1 + - - +
244C SER 5.1 1.0 - - - +
245C GLU* 2.7 42.4 + - - +
246C LEU* 3.7 22.9 - - + +
247C GLU* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 4.4 27.3 - - + +
34B ALA* 5.1 6.1 - - - +
39B THR* 4.9 7.8 + - - -
23C TYR 4.9 3.2 + - - +
24C LEU 3.4 0.6 - - - -
25C ARG* 1.3 101.8 + - - +
27C ALA* 1.3 63.1 + - - +
29C LYS* 3.4 4.8 + - - +
30C VAL* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 5.3 10.8 - - + -
30B VAL* 4.4 10.4 - - + +
23C TYR 5.5 0.6 + - - +
24C LEU* 3.3 19.0 + - + +
26C ASP* 1.3 78.0 - - - +
28C VAL* 1.3 61.6 - - - +
30C VAL* 3.0 11.2 - - - +
31C THR* 2.8 31.3 + - - +
411C LEU* 4.4 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 2.9 25.1 + - + +
25C ARG 3.7 4.5 - - - +
27C ALA* 1.3 76.4 - - - +
29C LYS* 1.3 58.0 + - - +
31C THR 3.3 0.3 + - - -
32C HIS* 2.8 28.9 + - - +
244C SER 4.3 5.6 - - - +
246C LEU* 4.2 17.3 - - + -
252C TYR* 3.5 35.4 - - + -
256C VAL* 3.6 30.3 - - + -
407C MSE 3.4 21.1 - - + +
411C LEU* 4.3 5.4 - - + -
----------------------------------------------------------
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 ARG* 3.0 43.6 + - - +
26C ASP* 3.8 5.8 - - - +
27C ALA 3.3 0.2 - - - -
28C VAL* 1.3 76.8 - - - +
30C VAL* 1.3 61.2 + - - +
32C HIS* 3.3 4.9 + - - +
33C HIS* 3.1 41.7 + - + +
244C SER* 3.1 44.7 + - - +
245C GLU* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 4.0 39.4 - - + +
27B ALA* 5.1 0.9 - - - +
30B VAL* 4.1 22.4 - - + -
26C ASP 3.2 11.2 + - - +
27C ALA* 3.0 26.2 - - - +
29C LYS* 1.3 77.9 - - - +
31C THR* 1.3 64.1 + - - +
33C HIS* 3.4 9.9 + - + +
34C ALA* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 5.7 2.7 - - - +
27C ALA* 2.8 23.1 + - - +
28C VAL 3.7 3.8 - - - -
29C LYS 3.2 0.2 - - - -
30C VAL* 1.3 77.1 - - - +
32C HIS* 1.3 66.1 + - - +
34C ALA* 3.1 8.4 + - + +
35C ILE* 3.0 22.9 + - + +
407C MSE 3.6 23.8 - - + -
410C TYR* 3.5 42.9 - - + +
411C LEU* 4.5 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL 2.8 18.3 + - - +
29C LYS 3.5 4.7 - - - +
31C THR* 1.3 77.1 - - - +
33C HIS* 1.3 79.3 + + - +
35C ILE* 3.1 14.2 + - - +
36C HIS* 3.1 48.5 + + - +
242C GLY 3.1 34.1 + - - -
243C THR 3.8 3.6 - - - -
244C SER* 3.3 27.4 - - - -
252C TYR* 2.6 37.5 + - + +
407C MSE 3.8 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 3.1 36.1 + - + +
30C VAL* 3.8 9.9 - - + +
31C THR 3.2 0.2 - - - -
32C HIS* 1.3 96.9 - + - +
34C ALA* 1.3 57.2 + - - +
36C HIS* 3.4 4.9 + - - +
37C GLU* 2.8 55.0 + - - +
244C SER* 4.3 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 4.4 13.2 - - - +
30C VAL 3.1 12.8 + - - +
31C THR* 3.1 13.6 + - + +
33C HIS* 1.3 72.3 - - - +
35C ILE* 1.3 62.2 + - + +
37C GLU* 4.6 0.7 - - - -
38C LYS* 2.9 22.5 + - - -
39C THR* 3.1 32.2 + - - +
40C GLY* 4.0 14.0 + - - +
46C LEU* 4.6 1.0 - - - +
410C TYR* 5.3 6.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C THR 3.0 18.1 + - - +
32C HIS* 3.1 8.5 + - - +
34C ALA* 1.3 80.6 - - - +
36C HIS* 1.3 72.7 + - + +
38C LYS* 3.3 9.5 + - - +
46C LEU* 3.6 25.7 - - + +
48C TRP* 5.2 2.5 - - + -
49C VAL* 4.0 26.4 - - + +
252C TYR* 4.6 8.5 - - + +
403C LYS* 4.4 11.2 - - + -
406C ALA* 4.0 22.2 - - + -
407C MSE 4.2 26.5 - - + +
410C TYR* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C HIS* 3.1 44.3 + + - +
33C HIS* 4.2 5.6 - - - +
35C ILE* 1.3 82.7 - - + +
37C GLU* 1.3 58.9 + - + +
38C LYS* 3.3 10.5 + - - +
49C VAL* 3.7 26.1 - - + +
50C ASP* 5.0 8.3 + - - -
238C ARG* 6.0 4.7 - - + -
242C GLY* 4.9 8.7 - - - -
399C TYR* 5.3 0.9 - - - -
403C LYS* 3.0 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C HIS* 2.8 46.3 + - + +
34C ALA* 5.1 0.2 - - - -
36C HIS* 1.3 73.9 - - + +
38C LYS* 1.3 71.5 + - - +
39C THR* 3.4 27.9 + - + +
----------------------------------------------------------
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