Contacts of the helix formed by residues 17 - 23 (chain C) in PDB entry 5F0L
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 ASN 17 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLY* 5.6 0.8 - - - -
14C LYS* 6.2 1.3 - - - +
15C PRO 3.5 5.0 + - - -
16C GLN* 1.3 73.4 - - - +
18C LEU* 1.3 62.1 + - - +
19C ASN* 2.8 48.7 + - - +
20C ASP* 3.1 24.6 + - - +
21C ALA* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLU* 3.8 28.0 - - + +
249A GLN* 3.9 16.4 - - - +
252A ASN* 3.2 46.4 - - + +
510A EDO 3.5 36.8 - - - -
16C GLN 3.4 1.8 + - - +
17C ASN* 1.3 73.5 + - - +
19C ASN* 1.3 62.0 + - - +
21C ALA* 3.9 2.9 - - - -
22C TYR* 3.3 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASN* 2.8 26.6 + - - +
18C LEU* 1.3 70.6 - - - +
20C ASP* 1.3 63.6 + - - +
23C GLY* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 3.5 15.6 - - - +
242B LYS* 3.5 55.4 + - + +
243B GLY* 4.9 3.5 - - - -
16C GLN* 4.1 5.2 - - + +
17C ASN* 3.1 27.1 + - - +
19C ASN* 1.3 80.3 - - - +
21C ALA* 1.3 64.0 + - - +
22C TYR 3.4 0.3 + - - -
23C GLY 3.8 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LYS* 3.2 25.5 - - + +
196A ARG* 3.5 12.5 + - - +
510A EDO 3.5 25.6 - - - -
241B VAL* 4.6 0.7 - - - +
16C GLN* 3.2 31.6 - - + +
17C ASN 3.0 13.2 + - - +
18C LEU* 4.0 6.7 - - - +
19C ASN 3.3 0.2 - - - -
20C ASP* 1.3 77.7 - - - +
22C TYR* 1.3 62.6 + - + +
23C GLY 4.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ALA 3.9 2.9 + - - -
191A ASN* 2.9 48.4 + - - +
192A LYS* 3.7 14.8 - - + -
195A VAL* 3.9 28.9 - - + +
196A ARG* 5.7 2.3 + - - -
199A HIS* 4.7 6.8 - - - -
249A GLN* 2.7 39.0 + - - +
252A ASN 3.7 9.0 - - - +
253A CYS* 3.4 47.0 - - + +
510A EDO 4.6 2.9 - - - -
18C LEU* 3.3 34.2 + - + +
21C ALA* 1.3 79.3 - - + +
23C GLY* 1.3 71.0 + - - +
24C PRO* 3.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 5.4 3.1 - - - +
18C LEU 4.5 0.2 + - - -
19C ASN* 2.8 24.1 + - - +
20C ASP 3.8 10.4 - - - +
21C ALA 4.8 0.7 - - - +
22C TYR* 1.3 78.4 - - - +
24C PRO* 1.3 77.9 - - - +
25C PRO* 3.7 2.4 - - - +
----------------------------------------------------------
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