Contacts of the strand formed by residues 43 - 50 (chain C) in PDB entry 2W4V
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 PHE 43 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 3.3 27.8 - - + -
36C VAL 3.4 6.5 - - - +
37C PRO* 4.3 17.9 - - + -
38C ASP* 3.7 4.0 - - - +
41C GLU* 2.7 38.7 + - - +
42C GLY* 1.3 89.9 - - - +
44C ALA* 1.3 60.7 + - - +
75C GLN* 4.3 22.4 - - + -
96C GLU* 3.7 26.2 - - + -
97C ALA* 3.2 24.9 - - + -
100C LEU* 4.7 4.0 - - + -
688C LEU* 2.7 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C CYS 3.5 1.9 - - - +
35C TRP* 3.5 5.1 - - - -
36C VAL* 2.6 50.9 + - + +
38C ASP* 4.0 17.0 - - - +
41C GLU* 5.4 1.1 - - + -
43C PHE* 1.3 75.4 - - - +
45C SER* 1.3 66.3 + - - +
46C ALA 3.2 0.7 + - - -
60C ILE* 5.5 8.7 - - + -
67C ARG* 3.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASN* 4.9 6.3 - - - +
34C CYS 3.8 4.9 - - - -
35C TRP* 5.2 7.2 - - - +
44C ALA* 1.3 70.0 - - - +
46C ALA* 1.3 59.3 + - - +
60C ILE* 3.8 4.5 - - - +
61C VAL* 3.1 43.7 + - - +
62C ALA* 4.4 5.9 + - - +
77C MET* 5.5 10.5 - - - -
101C TYR* 6.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LYS 4.1 0.2 - - - -
33C ASN* 2.7 26.5 + - - +
34C CYS* 2.8 27.2 + - + +
36C VAL* 3.3 41.3 - - + -
44C ALA 3.2 0.4 + - - -
45C SER* 1.3 75.2 - - - +
47C GLU* 1.3 57.4 + - - +
58C VAL* 3.8 17.0 - - + -
59C LYS 3.4 7.6 - - - +
60C ILE* 5.1 0.9 - - - -
61C VAL* 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LYS* 2.5 46.4 - - + -
33C ASN* 4.8 3.4 - - + +
46C ALA* 1.3 74.2 - - - +
48C ILE* 1.3 52.9 + - - +
49C GLN* 2.6 36.9 + - - +
58C VAL* 4.1 1.3 - - - -
59C LYS* 2.4 51.9 + - - +
61C VAL* 4.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LYS* 2.7 15.5 - - + +
32C LYS* 2.3 91.9 + - + +
34C CYS* 5.1 10.3 - - + -
46C ALA 5.7 0.2 - - - -
47C GLU* 1.3 71.6 - - - +
49C GLN* 1.3 62.3 + - - +
50C SER 5.0 2.5 - - - +
56C ILE* 5.0 6.3 - - + -
57C THR 4.7 0.4 - - - +
58C VAL* 3.8 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LYS* 3.8 11.1 + - - +
47C GLU* 2.6 38.1 + - - +
48C ILE* 1.3 77.1 - - - +
50C SER* 1.3 60.9 + - - +
57C THR* 2.6 26.2 + - - +
58C VAL 4.2 2.0 - - - -
59C LYS* 3.5 22.6 - - + +
66C THR* 5.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 5.0 1.7 - - - +
49C GLN* 1.3 80.9 - - - +
51C SER* 1.3 72.5 + - - +
56C ILE* 3.6 1.7 - - - -
57C THR* 2.9 49.6 + - - +
----------------------------------------------------------
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