Contacts of the strand formed by residues 130 - 136 (chain C) in PDB entry 4BEJ
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 130 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR* 5.8 0.4 - - + -
61C ARG* 3.5 48.2 - - - +
62C PRO 2.6 17.4 + - - +
63C LEU* 3.6 19.9 - - + +
64C ILE* 2.6 33.8 + - - +
93C PHE* 4.4 23.3 - - + -
95C HIS* 5.3 6.3 - - + -
111C ILE* 4.3 22.0 - - + -
114C GLU* 4.2 16.8 - - + +
115C THR* 4.4 6.7 - - - +
129C PRO* 1.3 72.0 - - - +
131C HIS* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLN* 3.6 16.0 + - + -
13C ASP* 3.0 35.4 - - - +
16C ASN* 3.1 37.2 + - + +
64C ILE* 3.2 33.3 - - + +
66C GLN* 4.5 7.9 - - - +
92C LYS 3.7 1.0 - - - +
93C PHE* 3.3 3.7 - - - -
94C LEU* 3.0 40.7 + - + +
95C HIS* 6.0 1.0 - - - -
129C PRO* 3.3 28.1 + - + +
130C ILE* 1.3 76.0 - - - +
132C LEU* 1.3 61.2 + - - +
133C LYS* 4.0 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 3.9 19.5 - - + -
63C LEU* 4.0 19.5 - - + -
64C ILE 3.1 6.8 + - - +
65C LEU* 3.7 11.1 - - + +
66C GLN* 2.9 26.9 + - - +
91C GLY 4.8 1.3 - - - -
92C LYS 3.4 19.7 - - - +
93C PHE* 3.5 40.6 - - + -
107C ILE* 3.7 27.8 - - + -
111C ILE* 6.1 3.6 - - + -
130C ILE 3.7 0.4 + - - -
131C HIS* 1.3 73.9 - - - +
133C LYS* 1.3 64.7 + - - +
134C ILE* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN* 5.4 6.7 - - - +
10C LYS* 6.3 0.4 - - - +
13C ASP* 4.3 12.5 + - - -
66C GLN* 3.3 32.1 + - - +
68C VAL* 4.1 16.2 - - + -
91C GLY* 3.2 2.4 - - - -
92C LYS* 2.5 54.7 + - + +
131C HIS 5.3 0.9 - - - +
132C LEU* 1.3 74.9 - - - +
134C ILE* 1.3 63.4 + - - +
135C PHE* 3.5 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 3.8 19.7 - - + -
50C LEU* 3.3 37.7 - - + -
65C LEU* 3.8 18.8 - - + -
66C GLN 2.9 6.5 + - - -
67C LEU* 3.6 12.3 - - + +
68C VAL* 2.9 26.9 + - - +
90C TRP 3.4 9.4 - - - +
91C GLY* 4.7 4.0 - - - -
104C PHE* 4.0 18.6 - - + -
107C ILE* 5.4 1.3 - - + -
132C LEU* 4.3 12.6 - - + -
133C LYS* 1.3 79.3 - - - +
135C PHE* 1.3 73.4 + - - +
136C SER* 4.0 7.7 + - - -
139C VAL* 4.9 1.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C VAL* 3.5 25.1 - - + -
70C VAL* 3.6 22.7 - - + -
89C GLU* 3.5 2.6 - - - -
90C TRP* 2.6 94.2 + + + +
91C GLY* 5.2 0.2 - - - -
92C LYS* 4.5 9.6 - - + -
133C LYS* 3.5 37.7 - - + -
134C ILE* 1.3 76.6 - - - +
136C SER* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 5.1 0.9 - - - -
68C VAL 3.3 5.9 + - - -
69C HIS* 3.4 1.4 - - - -
70C VAL* 3.2 21.2 + - - +
88C GLU 4.3 0.2 - - - -
89C GLU* 2.8 32.4 + - - -
134C ILE* 4.0 8.2 + - - -
135C PHE* 1.3 77.2 - - - +
137C PRO* 1.3 69.7 - - - +
138C ASN* 3.0 12.5 + - - +
139C VAL* 3.4 36.3 - - - +
----------------------------------------------------------
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