Contacts of the strand formed by residues 44 - 49 (chain C) in PDB entry 3A98
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 TRP 44 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C TRP* 4.0 15.3 - - + -
19C PHE* 3.8 17.0 - + - -
26C GLN* 4.1 15.0 - - + -
40C THR* 3.5 3.1 - - - -
41C CYS 3.0 36.0 + - - +
42C GLY 3.3 1.2 + - - -
43C ASP* 1.3 87.1 - - + +
45C TYR* 1.3 60.8 + - - +
58C ILE* 3.8 16.6 - - + -
59C PHE* 3.3 32.8 - - - -
60C PRO* 3.5 26.0 - - + -
61C LYS* 3.6 11.0 - - - -
713D ILE* 4.8 4.3 - - + -
714D PRO* 3.6 33.3 - - + +
715D LYS 2.9 21.6 + - - -
716D GLU* 3.8 12.3 - - + -
717D PRO* 3.6 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C TRP* 3.9 3.1 - - - -
10C GLU* 2.9 37.2 + - + -
37C ILE* 3.4 31.4 - - + -
39C GLU 3.2 4.5 - - - +
40C THR* 3.7 11.7 - - - -
44C TRP* 1.3 75.0 - - - +
46C ARG* 1.3 59.8 - - - +
58C ILE* 3.2 25.8 - - - +
59C PHE* 2.9 41.0 + + + +
61C LYS* 3.4 59.8 + - + +
64C ILE* 3.9 13.6 + - + -
66C ILE* 3.3 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C TRP* 3.6 16.4 - - + -
37C ILE* 3.8 1.4 - - - -
38C GLN* 2.8 26.7 + - - +
39C GLU* 2.9 38.9 + - + +
45C TYR* 1.3 75.1 - - - +
47C GLY* 1.3 61.1 + - - +
56C GLN* 3.6 33.0 - - + +
57C GLY* 3.3 17.0 - - - +
58C ILE* 3.9 6.7 - - + -
59C PHE* 4.3 2.7 - - - -
722D PHE* 3.2 48.7 - - - +
724D TYR* 2.9 34.6 + - - +
726D CYS* 3.6 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.1 0.5 - - - +
36C ARG 3.1 15.5 - - - -
38C GLN* 3.6 15.3 - - - -
46C ARG* 1.3 76.9 - - - +
48C TYR* 1.3 61.6 + - - -
56C GLN* 3.2 3.8 - - - +
57C GLY 2.8 33.0 + - - +
59C PHE* 3.6 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.4 2.5 - - - -
35C VAL* 3.3 7.9 - - - -
36C ARG* 2.9 76.0 + - + +
38C GLN* 3.6 28.3 - - + -
47C GLY* 1.3 75.0 - - - +
49C LEU* 1.3 72.0 + - - +
50C ILE* 3.9 2.4 - - + +
53C LYS* 3.6 51.6 + - + +
55C LEU 3.2 15.9 - - - +
56C GLN* 3.7 5.4 - - + -
59C PHE* 4.6 0.6 - - - -
727D ASN* 3.2 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.3 13.7 - - + -
28C SER 5.3 2.2 - - - +
29C LEU* 3.9 10.3 - - + -
33C ASP* 3.6 39.9 - - + +
34C VAL 3.7 5.2 - - - +
35C VAL* 3.8 15.5 - - + -
48C TYR* 1.3 72.4 - - - +
50C ILE* 1.3 61.9 + - - +
51C LYS* 4.4 2.2 - - + +
52C HIS* 2.8 52.1 + - + +
53C LYS* 3.0 5.4 + - - -
55C LEU* 3.2 32.8 + - + +
----------------------------------------------------------
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