Contacts of the strand formed by residues 70 - 76 (chain B) in PDB entry 4FPR
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 MET 70 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 3.5 11.8 + - - +
52B THR* 4.0 20.6 - - + +
55B LEU* 3.6 44.0 - - - +
56B ILE* 3.8 19.7 - - + +
66B TRP* 3.6 39.5 - - + +
67B GLY 3.7 10.8 - - - +
68B ILE 3.3 5.5 + - - -
69B ASP* 1.3 79.6 + - - +
71B THR* 1.3 70.5 + - - +
94B ILE* 4.0 18.6 - - + -
95B THR 3.1 6.3 - - - +
96B ALA* 3.8 11.4 - - + -
131B TRP* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.0 28.5 - - + +
42A THR* 4.2 4.5 - - - +
45A LEU* 4.1 22.7 - - + -
74A VAL* 6.1 0.7 - - + -
52B THR* 4.9 1.8 - - - -
70B MET* 1.3 81.4 - - - +
72B ALA* 1.3 61.0 + - - +
73B LYS* 5.9 2.6 - - - +
93B LYS 3.8 1.2 - - - +
94B ILE* 3.4 4.0 - - - -
95B THR* 2.8 40.8 + - - -
97B HIS* 2.6 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.7 12.4 - - - +
72A ALA 5.2 3.8 - - - +
45B LEU* 4.0 10.5 - - + +
48B CYS* 3.8 20.2 - - - -
49B ASN* 3.4 23.4 + - - +
52B THR* 3.3 24.4 + - - +
71B THR* 1.3 74.7 - - - +
73B LYS* 1.3 69.5 + - - +
93B LYS 3.5 3.8 - - - +
94B ILE* 4.4 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 5.7 1.1 - - - +
73A LYS* 4.1 43.3 - - + +
45B LEU* 4.1 5.8 - - - -
48B CYS* 3.6 5.1 - - - -
71B THR* 5.9 2.5 - - - +
72B ALA* 1.3 77.9 - - - +
74B VAL* 1.3 63.0 + - - +
75B GLN* 6.2 1.6 - - + -
93B LYS* 2.9 53.1 + - + +
95B THR* 5.6 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 6.0 2.2 - - + -
73A LYS* 5.9 3.3 - - - +
41B LYS* 4.4 9.2 - - + +
44B ALA* 4.2 14.6 - - + +
45B LEU* 3.6 37.2 - - + +
48B CYS* 4.3 10.5 - - + -
73B LYS* 1.3 77.7 - - - +
75B GLN* 1.3 72.3 + - - +
76B CYS* 4.2 7.2 - - - -
90B CYS* 4.0 22.4 - - + -
91B THR 3.2 15.5 - - - +
92B CYS* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 5.4 6.9 + - - +
73B LYS* 6.2 1.1 - - + -
74B VAL* 1.3 83.4 - - - +
76B CYS* 1.3 64.2 + - - +
90B CYS* 3.3 1.9 - - - -
91B THR* 2.8 33.7 + - - +
136C LYS* 3.4 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PRO* 5.3 2.7 - - + -
40B THR 6.3 0.2 - - - -
41B LYS* 3.9 29.3 + - + +
44B ALA* 3.6 21.8 - - - -
74B VAL* 4.2 4.7 - - - -
75B GLN* 1.3 76.3 - - - +
77B ALA* 1.3 71.6 + - - +
78B PRO* 3.6 3.8 - - - +
88B VAL* 4.3 3.4 - - + -
89B LEU 3.5 3.6 - - - -
90B CYS* 2.0 44.9 - - - -
136C LYS* 3.6 9.3 - - - +
----------------------------------------------------------
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