Contacts of the strand formed by residues 46 - 51 (chain B) in PDB entry 3F12
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 GLU 46 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 4.7 0.9 - - - +
37B VAL* 3.6 3.4 - - - -
38B ARG* 2.7 80.5 + - - +
40B ALA* 5.8 3.6 - - - +
44B GLY 5.3 0.4 - - - +
45B LEU* 1.3 76.5 - - - +
47B TRP* 1.3 69.1 + - - +
48B VAL* 5.4 0.9 - - - -
63B SER* 4.1 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 3.8 15.5 - - + -
96A PRO* 3.4 31.6 - - + -
97A TRP* 2.6 65.3 + + + +
99A PHE* 4.3 9.6 - - + -
35B HIS* 3.4 10.6 + + - -
36B TRP 3.2 20.9 - - - -
37B VAL* 3.5 17.5 - - + +
45B LEU 4.3 0.2 - - - -
46B GLU* 1.3 83.7 - - - +
48B VAL* 1.3 58.0 + - - +
49B ALA* 2.8 41.1 + - - -
50B VAL* 3.8 1.3 - - + -
59B TYR 3.6 8.7 - - - -
60B TYR 3.5 22.0 - - - -
61B ALA* 3.4 28.9 - - + +
112B LEU* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 2.6 25.8 + - + +
37B VAL 4.1 1.1 - - - -
38B ARG* 3.3 50.0 - - + +
46B GLU* 3.6 2.9 - - - +
47B TRP* 1.3 77.9 - - - +
49B ALA* 1.3 63.5 + - + +
61B ALA* 3.0 27.1 + - + +
64B VAL* 4.3 12.8 - - + +
68B PHE* 3.4 39.7 - - + -
81B LEU* 5.0 0.2 - - + -
94B TYR* 4.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B HIS* 3.6 1.7 - - - -
36B TRP* 3.0 28.7 + - + +
47B TRP* 2.8 29.2 + - - +
48B VAL* 1.3 85.2 - - + +
50B VAL* 1.3 58.1 + - - +
59B TYR 3.7 2.2 - - - +
60B TYR* 3.6 31.0 - - + +
70B ILE* 4.5 13.2 - - + -
81B LEU* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 3.8 26.5 - - + -
33B GLY* 5.1 1.6 - - - -
34B MET 3.0 16.8 - - - +
35B HIS* 3.5 22.0 - - + +
47B TRP* 4.5 0.2 - - + -
49B ALA* 1.3 76.2 - - - +
51B ILE* 1.3 77.3 + - - +
57B ASN 5.5 0.7 - - - +
58B LYS* 3.5 13.4 - - - +
59B TYR* 2.9 41.4 + - + +
70B ILE* 3.4 18.2 - - - +
99B ASP* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLY* 3.2 3.6 - - - -
34B MET* 2.8 53.8 + - + +
50B VAL* 1.3 84.1 - - - +
52B SER* 1.3 59.5 - - - +
55B GLY* 4.0 17.5 - - - -
57B ASN 3.7 9.6 - - - +
58B LYS* 3.2 36.6 - - + -
70B ILE* 3.4 24.0 - - + -
71B SER* 4.3 11.9 - - - +
72B ARG* 3.6 26.5 - - + -
79B LEU* 4.5 3.6 - - + -
----------------------------------------------------------
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