Contacts of the strand formed by residues 69 - 75 (chain C) in PDB entry 5LF4
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 VAL 69 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 4.0 0.2 - - - -
65C LEU* 2.9 33.6 + - + -
66C ASP* 3.1 14.7 + - + +
67C ASP 3.5 1.0 + - - -
68C ASN* 1.3 103.1 - - - +
70C CYS* 1.3 64.1 + - - +
91C CYS* 5.5 0.4 - - - -
102C VAL* 3.8 21.8 - - + +
104C VAL* 4.3 11.7 - - + -
107C ILE* 3.9 13.7 - - + -
133C ILE* 3.7 24.9 - - + -
134C VAL 3.3 14.4 - - - +
211C MET* 4.1 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 4.0 10.3 - - + -
62C ILE* 4.9 1.6 - - + -
63C YCM 3.4 15.5 - - - +
64C ALA* 4.1 7.0 - - - -
65C LEU* 4.1 2.2 - - - +
69C VAL* 1.3 76.1 - - - +
71C MET* 1.3 66.5 + - - +
133C ILE* 3.5 4.7 - - - +
134C VAL* 2.9 55.7 + - - +
210C VAL 6.1 0.2 - - - -
211C MET* 3.6 24.7 - - + -
217C LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.9 6.7 - - - -
61C LYS 3.9 0.7 - - - +
62C ILE* 3.4 2.4 - - - +
63C YCM 2.8 35.5 + - + +
65C LEU* 3.9 28.7 - - + -
70C CYS* 1.3 81.1 - - - +
72C ALA* 1.3 68.6 + - - +
73C PHE* 4.0 16.2 - - + -
80C ALA 5.1 0.2 - - - +
83C VAL* 5.0 4.7 - - + -
84C ILE* 3.6 33.7 - - + -
111C ILE* 4.4 12.8 - - - -
129C ILE* 4.6 9.6 - - + -
131C ALA* 3.7 26.5 - - + -
132C LEU 3.1 11.9 - - - +
133C ILE* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA* 4.4 11.4 - - + -
43C LEU* 3.7 24.3 - - + +
44C GLY 5.6 0.2 - - - +
45C VAL* 4.3 11.4 - - + -
61C LYS 3.3 13.0 - - - +
62C ILE* 4.1 10.5 - - + -
71C MET* 1.3 77.6 - - - +
73C PHE* 1.3 62.1 + - - +
131C ALA* 3.2 6.9 - - - +
132C LEU* 2.8 33.0 + - + +
161C ILE* 5.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C SER 4.7 1.4 - - - +
32C ALA* 4.2 9.9 - - - +
45C VAL* 5.4 1.4 - - - +
60C ARG 4.7 3.4 - - - -
61C LYS* 3.6 56.5 + - + +
63C YCM 4.9 4.3 - - - -
71C MET* 4.0 11.9 - - + -
72C ALA* 1.3 78.7 - - - +
74C ALA* 1.3 72.2 + - - +
75C GLY 4.1 6.5 - - - -
77C THR* 3.7 39.0 - - + -
80C ALA* 3.5 32.3 - - + -
84C ILE* 4.4 15.7 - - + -
129C ILE* 4.5 6.3 - - + -
130C SER 3.2 13.9 - - - +
131C ALA* 4.2 0.2 - - - +
161C ILE* 4.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL* 3.7 10.0 - - + +
29C GLY* 4.6 0.9 - - - -
30C SER 3.3 26.5 - - - +
32C ALA* 4.9 0.7 - - + -
61C LYS* 5.8 1.3 - - - -
73C PHE* 1.3 78.4 - - - +
75C GLY* 1.3 58.6 + - - +
129C ILE* 3.4 3.6 - - - -
130C SER 3.1 29.6 + - - -
161C ILE* 3.7 12.8 - - + +
162C GLY* 3.7 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ALA 3.7 20.2 - - - -
26C VAL* 3.9 2.7 - - - -
29C GLY* 3.9 14.5 - - - -
30C SER 5.0 0.2 - - - +
73C PHE* 4.1 4.2 - - - -
74C ALA* 1.3 74.6 - - - +
76C LEU* 1.3 66.8 + - - -
77C THR* 3.3 13.0 + - - +
128C GLY 3.3 8.5 - - - -
129C ILE* 4.2 1.1 - - - -
----------------------------------------------------------
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