Contacts of the helix formed by residues 19 - 30 (chain B) in PDB entry 4HFX
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 THR 19 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG 3.9 2.0 + - - +
18B CYS* 1.3 76.8 - - - +
20B PRO* 1.4 67.9 - - + +
21B ASP* 2.8 25.8 + - - +
22B GLN* 2.7 37.0 + - - +
23B LEU* 2.9 25.5 + - - +
44B HIS* 4.2 1.3 - - - -
20C PRO* 5.0 8.3 - - + -
64C TYR* 3.5 21.8 + - - +
68C GLN* 4.6 0.2 + - - -
71C ARG* 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 1.4 90.0 - - + +
21B ASP* 1.3 58.7 + - - +
23B LEU* 4.4 0.7 - - + -
24B TYR* 3.0 28.8 + - - +
41B TRP* 3.3 19.1 - - + -
44B HIS* 3.6 32.1 - - + +
47B ARG* 5.2 4.5 - - - +
64B TYR* 3.3 41.3 - - + +
19C THR* 4.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 2.8 24.8 + - - -
20B PRO* 1.3 75.2 - - - +
22B GLN* 1.3 59.5 + - - +
24B TYR* 3.4 8.0 + - - +
25B ARG* 3.1 54.1 + - - +
19C THR* 4.1 5.7 - - - +
20C PRO* 4.1 11.6 - - - +
21C ASP* 3.7 38.1 + - - +
68C GLN* 3.5 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B CYS* 4.1 10.1 - - + -
19B THR* 2.7 42.2 + - - +
21B ASP* 1.3 76.4 - - - +
23B LEU* 1.3 64.9 + - - +
25B ARG* 3.2 24.3 + - - +
26B ILE* 3.0 30.0 + - - +
64C TYR* 4.6 3.2 + - - -
68C GLN* 3.1 34.8 + - + +
71C ARG* 3.3 42.1 + - - +
72C GLU* 4.5 8.0 - - + +
75C LEU* 5.3 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 3.7 45.8 - - + +
18B CYS* 4.0 7.5 - - + +
19B THR 2.9 15.9 + - - +
20B PRO 3.9 5.2 - - - +
22B GLN* 1.3 75.5 - - - +
24B TYR* 1.3 57.6 + - - +
26B ILE* 3.8 6.7 - - + +
27B GLU* 2.9 52.4 + - + +
40B LEU* 3.9 21.8 - - + -
41B TRP* 3.7 24.2 - - + +
44B HIS* 3.8 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PRO 3.0 18.5 + - - +
21B ASP* 3.6 7.6 - - - +
22B GLN 3.2 0.2 - - - -
23B LEU* 1.3 77.4 - - - +
25B ARG* 1.3 68.4 + - + +
27B GLU* 3.3 9.1 + - - +
28B GLU* 3.0 66.0 + - + +
41B TRP* 4.1 4.9 - + + -
61B ARG* 3.7 17.0 - - - -
65B LEU* 4.4 28.9 - - + -
76D ARG* 4.1 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP* 3.1 57.7 + - - +
22B GLN* 3.5 15.4 - - - +
24B TYR* 1.3 84.8 - - + +
26B ILE* 1.3 60.9 + - + +
28B GLU* 3.6 8.1 + - - +
29B TYR* 3.2 23.6 + - - +
21C ASP* 4.0 13.7 + - - +
68C GLN* 3.5 19.7 + - - +
72C GLU* 2.7 35.6 + - - +
76C ARG* 4.6 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 4.6 15.5 - - + -
18B CYS* 5.4 0.7 - - - -
22B GLN 3.0 20.0 + - - +
23B LEU* 3.8 7.2 - - + +
25B ARG* 1.3 80.5 - - + +
27B GLU* 1.3 61.1 + - + +
28B GLU 3.2 0.4 - - - -
29B TYR* 3.3 7.3 + - + +
30B ASN* 3.1 24.8 + - - +
33B LEU* 5.4 5.1 - - + +
72C GLU* 4.6 10.5 - - + +
75C LEU* 3.3 43.3 - - + -
76C ARG* 4.2 24.2 - - + +
79C THR* 3.6 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 6.4 0.4 - - + -
23B LEU* 2.9 34.7 + - + +
24B TYR 3.3 1.5 + - - +
26B ILE* 1.3 78.0 - - + +
28B GLU* 1.3 60.7 - - - +
30B ASN 3.0 23.0 - - - +
31B HIS* 3.5 9.7 - - - +
33B LEU* 4.1 21.9 - - + +
34B ILE* 3.9 19.2 - - + +
41B TRP* 3.1 41.0 + - - -
61B ARG* 3.2 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 5.3 5.6 - - - +
24B TYR* 3.0 66.1 + - + +
25B ARG* 3.8 8.5 - - - +
26B ILE 3.2 0.2 - - - -
27B GLU* 1.3 76.4 - - - +
29B TYR* 1.3 63.7 + - - +
30B ASN* 3.4 0.7 - - - -
31B HIS* 4.9 2.6 + - - +
61B ARG* 4.6 5.5 + - - +
76D ARG* 3.3 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 4.3 25.0 - - + +
25B ARG 3.2 14.2 + - - +
26B ILE* 3.3 12.8 + - - +
28B GLU* 1.3 79.0 - - - +
30B ASN* 1.3 62.2 + - + +
31B HIS 4.3 0.2 - - - -
76C ARG* 3.3 62.7 + - + +
79C THR* 3.2 30.1 - - - -
80C LYS* 3.4 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE 3.1 7.4 + - - +
27B GLU* 3.0 17.2 - - - +
29B TYR* 1.3 85.5 - - + +
31B HIS* 1.3 71.1 + - - +
32B VAL* 3.4 29.9 + - + +
33B LEU* 3.5 15.4 + - + +
79C THR* 2.9 32.2 + - - +
80C LYS 4.0 8.5 + - - -
81C ASN* 4.9 5.9 - - - +
----------------------------------------------------------
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