Contacts of the strand formed by residues 121 - 131 (chain E) in PDB entry 5FLX
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 TYR 121 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E VAL* 4.1 1.0 - - - +
100E ARG* 3.1 25.5 + - - +
117E GLU 3.8 18.4 - - - -
118E GLU* 2.7 13.6 + - - +
119E ALA 3.6 5.4 - - - +
120E LYS* 1.3 91.8 - - + +
122E LYS* 1.3 63.0 + - - +
161E GLN* 3.2 35.2 - - + +
162E ILE 4.0 2.2 - - - -
163E ASP* 4.6 22.2 - - + -
164E LEU* 5.1 0.4 - - - -
170E ILE* 5.5 9.2 - - + -
236E ILE* 5.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASP* 2.9 29.6 + - - +
86E PHE 5.1 0.9 - - - -
87E MET* 3.2 31.4 - - + +
88E ASP* 3.0 18.2 + - - +
89E VAL* 4.3 7.0 - - + -
121E TYR* 1.3 78.2 - - - +
123E LEU* 1.3 73.2 + - - +
124E CYS* 5.6 1.6 - - - -
142E HIS* 6.4 0.4 - - - -
143E ASP* 3.3 23.2 + - - -
145E ARG* 4.7 2.8 - - - +
161E GLN* 3.3 6.5 - - - +
162E ILE* 2.5 55.9 + - + +
164E LEU* 3.7 28.1 - - + +
236E ILE* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E MET* 3.5 34.9 - - + +
122E LYS* 1.3 86.9 - - - +
124E CYS* 1.3 62.9 + - - +
142E HIS* 4.9 1.9 - - - -
159E THR* 4.1 14.4 - - + -
160E VAL 3.6 3.1 - - - +
161E GLN* 3.7 37.0 - - + +
171E ASN 5.5 1.1 - - - +
226E PHE* 4.1 13.7 - - + -
227E VAL 4.9 0.2 - - - +
228E ILE* 4.1 21.1 - - + +
235E TRP* 4.0 26.7 - - + -
236E ILE* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E LYS* 5.6 2.0 - - - -
123E LEU* 1.3 75.9 - - - +
125E LYS* 1.3 59.4 + - - +
126E VAL* 6.2 1.3 - - - -
139E LEU* 6.0 2.0 - - - -
141E THR* 3.6 30.3 - - + -
142E HIS* 3.8 7.6 - - + -
143E ASP* 5.5 2.7 - - + -
145E ARG* 5.9 3.8 - - + -
159E THR* 3.2 2.9 - - - -
160E VAL* 2.7 64.5 + - - +
162E ILE* 3.8 28.7 - - + -
169E ILE* 4.7 7.9 - - - -
226E PHE* 3.9 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E CYS* 1.3 74.6 - - - +
126E VAL* 1.3 69.1 + - - +
127E ARG* 6.2 0.2 - - - +
141E THR* 3.3 28.5 - - - +
142E HIS* 3.1 28.2 + - + +
157E ASN* 3.9 30.2 - - - +
158E ASP 3.3 15.3 - - - +
159E THR* 4.7 0.7 - - - +
184E ILE* 5.4 5.8 - - + +
222E LEU 3.2 19.8 + - - -
223E SER* 4.4 6.9 + - - +
225E ILE* 2.3 38.4 + - - +
226E PHE* 3.5 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E CYS* 5.3 1.3 - - - +
125E LYS* 1.3 79.8 - - - +
127E ARG* 1.3 61.7 + - - +
128E LYS 3.8 17.5 - - - +
129E ILE* 4.7 3.8 - - + +
139E LEU* 3.5 43.3 - - + -
140E VAL 3.4 2.7 - - - -
142E HIS* 6.2 0.2 - - - -
154E ILE* 3.6 18.2 - - + -
155E LYS 4.2 7.6 - - - +
156E VAL* 2.8 34.4 - - - +
157E ASN* 3.8 9.2 + - - -
158E ASP* 3.0 14.5 + - + +
160E VAL* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3441 U 3.7 46.0 + - - -
3451 U 4.6 9.7 + - - -
35E PRO 5.1 1.6 + - - -
37E LYS* 6.0 5.3 - - - +
125E LYS* 3.6 3.6 + - - +
126E VAL* 1.3 75.1 - - - +
128E LYS* 1.3 65.3 + - + +
140E VAL* 2.5 33.9 + - + +
141E THR 4.0 3.2 + - - -
142E HIS* 3.4 45.1 + - + +
156E VAL* 4.1 11.4 - - - +
157E ASN* 4.6 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3431 A 3.4 53.3 + - - -
3441 U 4.3 6.9 + - - +
126E VAL* 3.6 8.3 - - - +
127E ARG* 1.3 85.4 - - + +
129E ILE* 1.3 63.8 + - - +
130E THR* 5.9 6.7 - - + -
139E LEU* 3.7 1.0 - - - -
140E VAL* 2.8 51.1 + - + +
156E VAL* 4.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2881 G 5.1 12.4 + - - +
2891 G 4.9 14.7 - - - +
126E VAL* 4.9 7.9 - - + -
128E LYS* 1.3 78.3 - - - +
130E THR* 1.3 70.4 + - - +
131E VAL* 6.3 0.2 - - + -
137E PRO* 5.5 8.5 - - + -
138E HIS 3.3 16.4 - - - +
139E LEU* 5.0 7.0 - - + -
150E PRO* 5.9 2.9 - - + -
151E ASP 4.6 14.6 - - - +
152E PRO* 5.6 2.7 - - + +
154E ILE* 4.1 22.7 - - + +
155E LYS 5.8 0.2 - - - +
156E VAL* 4.2 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2881 G 5.8 2.2 - - - -
2961 U 4.0 10.7 + - - -
3421 C 5.5 7.0 - - - +
128E LYS* 5.9 7.0 - - + -
129E ILE* 1.3 79.5 - - - +
131E VAL* 1.3 74.7 + - - +
132E GLY* 6.0 0.2 - - - -
137E PRO* 3.4 1.6 - - - +
138E HIS* 2.5 55.6 + - + +
140E VAL* 5.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2871 U 4.6 12.1 - - - +
2881 G 4.9 22.7 - - - +
2961 U 3.2 34.4 + - + +
2971 A 3.4 27.1 + - - +
129E ILE* 6.3 0.4 - - + -
130E THR* 1.3 86.5 + - - +
132E GLY* 1.3 60.3 + - - +
135E GLY* 4.7 7.2 - - - +
136E ILE 3.3 8.1 - - - +
137E PRO* 3.9 20.2 - - + -
138E HIS* 4.1 0.7 - - - -
----------------------------------------------------------
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