Contacts of the strand formed by residues 128 - 133 (chain B) in PDB entry 3DAE
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 ILE 128 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LYS 3.4 0.5 - - - +
86B ILE* 2.7 54.7 + - + +
100B ILE* 4.6 13.9 - - + -
101B GLU* 4.3 18.6 - - - +
104B ILE* 4.1 20.4 - - + -
121B VAL* 4.2 4.9 - - + -
122B ILE 3.6 3.1 - - - -
123B LYS* 4.1 28.0 - - + +
124B SER 5.4 1.3 - - - +
126B ASP 5.0 2.7 - - - +
127B GLU* 1.3 77.2 - - - +
129B ILE* 1.3 62.1 + - - +
130B MET* 4.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 6.0 5.2 - - + -
83B LEU* 4.2 32.5 - - + -
84B LYS 3.6 5.8 - - - +
85B ILE* 4.4 17.7 - - + -
121B VAL* 3.5 4.0 - - - +
122B ILE* 2.7 64.1 + - + +
127B GLU* 4.2 31.9 - - + +
128B ILE* 1.3 77.4 - - - +
130B MET* 1.3 65.1 + - - +
131B VAL* 3.8 2.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA 3.1 7.6 - - - +
83B LEU* 3.4 2.6 - - - -
84B LYS* 3.0 50.9 + - + +
86B ILE* 4.3 20.6 - - + -
100B ILE* 4.5 5.6 - - - +
103B GLU* 4.4 11.2 - - + +
104B ILE* 3.8 40.6 - - + +
107B LEU* 4.3 17.7 - - + -
118B LEU* 4.0 19.5 - - + -
120B ASP 3.9 2.7 - - - -
121B VAL* 4.8 2.5 - - + +
128B ILE* 4.6 6.3 - - + -
129B ILE* 1.3 74.7 - - - +
131B VAL* 1.3 61.2 + - - +
132B ILE* 3.6 12.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 3.5 35.7 - - + +
81B VAL* 3.6 21.8 - - + -
82B ALA 3.8 2.0 - - - -
83B LEU* 4.0 14.6 - - + -
118B LEU* 3.1 10.8 - - - +
119B TYR* 2.8 35.0 + - + -
120B ASP* 2.6 41.7 + - + +
122B ILE* 4.6 14.1 - - + -
129B ILE* 4.7 2.5 - - + +
130B MET* 1.3 72.3 - - - +
132B ILE* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 3.3 9.6 - - - +
82B ALA* 2.7 48.4 + - + +
84B LYS* 3.3 43.7 - - + -
107B LEU* 4.8 8.5 - - + -
116B ILE* 3.8 25.1 - - + -
117B LYS 3.3 9.2 - - - +
118B LEU* 4.6 5.4 - - + -
119B TYR* 4.2 0.4 - - - -
130B MET* 4.0 21.8 - - + +
131B VAL* 1.3 79.1 - - - +
133B GLU* 1.3 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLN* 4.1 10.2 + - - +
80B LYS 4.4 0.4 - - - -
82B ALA* 5.2 0.9 - - - +
115B ILE 4.0 0.2 - - - +
116B ILE* 3.3 34.0 - - + +
117B LYS* 2.7 53.4 + - + +
119B TYR* 3.6 31.6 + - + +
132B ILE* 1.3 74.7 - - - +
134B TYR* 1.3 67.2 - - - +
135B ALA* 3.6 1.9 + - + -
184B LEU* 5.6 0.3 - - - +
186B ASP* 5.9 1.0 - - - +
192B LYS* 3.4 30.3 + - - +
----------------------------------------------------------
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