Contacts of the helix formed by residues 19 - 26 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PRO* 4.7 12.6 - - + -
21B ASP* 4.1 12.9 - - + +
64B TYR* 4.3 9.9 - - - +
68B GLN* 4.1 21.0 + - - +
71B ARG* 5.8 0.2 - - - +
17C ARG 3.6 3.5 + - - +
18C CYS* 1.3 75.5 - - - +
20C PRO* 1.4 71.9 - - + +
21C ASP* 2.4 26.1 + - - -
22C GLN* 3.1 17.9 + - - +
23C LEU* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 5.0 6.5 - - + -
20B PRO* 6.4 0.2 - - + -
21B ASP* 4.1 14.6 - - - +
18C CYS 4.6 0.9 - - - +
19C THR* 1.4 87.9 - - + +
21C ASP* 1.3 57.1 + - - +
23C LEU* 3.6 13.8 - - + +
24C TYR* 2.9 30.1 + - - +
64C TYR* 3.6 44.2 - - + +
65C LEU* 6.0 2.8 - - + +
68C GLN* 4.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP* 3.7 32.6 + - + +
25B ARG* 4.0 11.8 + - - +
72B GLU* 4.5 5.4 - - - +
19C THR* 2.4 30.2 + - - -
20C PRO* 1.3 75.5 - - - +
22C GLN* 1.3 78.1 + - - +
24C TYR* 3.7 7.4 - - - +
25C ARG* 3.0 29.1 + - - +
68C GLN* 5.6 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLN* 2.5 32.3 + - - +
71B ARG* 3.7 13.6 - - - +
72B GLU* 2.8 44.5 + - + +
75B LEU* 3.8 11.7 - - + +
18C CYS* 3.6 26.1 - - + -
19C THR* 3.1 14.8 + - - +
21C ASP* 1.3 90.1 + - - +
23C LEU* 1.3 65.4 + - - +
25C ARG* 3.5 5.3 + - - +
26C ILE* 3.2 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 3.9 40.6 - - + +
18C CYS* 4.1 8.0 - - + +
19C THR 2.9 15.8 + - - +
20C PRO* 3.6 12.3 - - + +
22C GLN* 1.3 77.8 - - - +
24C TYR* 1.3 58.1 + - - +
26C ILE* 2.8 34.2 + - - +
27C GLU* 3.4 24.8 - - - +
37C THR* 4.4 21.1 - - - +
61C ARG* 6.1 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PRO 2.9 20.3 + - - +
21C ASP* 3.7 7.4 - - - +
23C LEU* 1.3 72.9 - - - +
25C ARG* 1.3 72.2 + - + +
26C ILE 3.1 0.9 + - - -
27C GLU* 3.3 28.4 - - - +
61C ARG* 3.1 33.9 + - - +
65C LEU* 3.6 36.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
21C ASP 3.0 18.8 + - - +
22C GLN* 3.7 7.4 - - - +
23C LEU 3.4 0.2 - - - -
24C TYR* 1.3 80.9 - - + +
26C ILE* 1.3 59.5 + - + +
27C GLU 3.0 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.9 36.1 - - + -
79B THR* 3.9 34.5 - - + +
11C LEU* 5.7 1.8 - - + -
15C LEU* 4.2 25.5 - - + +
18C CYS* 4.5 0.7 - - - -
22C GLN 3.2 17.5 - - - +
23C LEU* 2.8 17.2 + - - +
24C TYR 3.1 0.4 - - - -
25C ARG* 1.3 74.4 - - + +
27C GLU* 1.3 70.1 + - - +
34C ILE 5.3 1.4 + - - -
----------------------------------------------------------
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