Contacts of the strand formed by residues 134 - 142 (chain B) 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 LEU 134 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 4.3 16.4 - - + +
127B VAL 3.8 13.2 - - - +
128B LYS* 3.9 27.1 - - + +
132B GLY 3.4 4.3 + - - +
133B TYR* 1.3 74.0 - - - +
135B LEU* 1.3 74.9 + - - +
217B MET* 4.0 3.0 - - - +
218B LEU* 3.4 28.6 + - + -
219B LYS* 3.3 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 3.6 5.7 - - - +
127B VAL* 3.3 41.0 + - + +
129B THR* 4.7 15.0 - - + -
134B LEU* 1.3 82.8 - - - +
136B ARG* 1.3 60.9 + - - +
137B LEU* 3.6 28.0 - - + -
176B VAL* 5.5 4.0 - - + -
184B VAL* 6.0 6.3 - - + -
215B VAL* 3.6 25.4 - - + -
216B LYS 3.3 15.9 - - - +
217B MET* 3.5 32.3 - - + -
218B LEU* 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9411 C 2.5 46.2 + - - -
9421 G 3.0 42.7 + - - -
124B HIS* 5.9 0.7 - - + -
125B VAL 5.0 0.4 - - - +
126B ASP* 3.2 23.9 + - - +
135B LEU* 1.3 73.6 - - - +
137B LEU* 1.3 60.7 + - - +
138B PHE* 3.8 20.4 - - + -
214B LYS 4.0 0.9 - - - +
215B VAL* 3.3 4.9 - - - -
216B LYS* 3.0 47.7 + - + +
218B LEU* 3.5 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B HIS* 3.8 1.1 - - - +
125B VAL* 3.3 41.7 + - + +
127B VAL* 3.7 16.6 - - + -
135B LEU* 3.6 19.1 - - + -
136B ARG* 1.3 73.3 - - - +
138B PHE* 1.3 76.0 + - - +
172B MET* 3.5 38.8 - - + -
176B VAL* 5.0 10.8 - - + -
193B ILE* 6.6 0.2 - - + -
212B VAL* 5.6 2.0 - - + +
214B LYS 3.6 4.0 - - - -
215B VAL* 3.6 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9411 C 4.2 7.6 - - - -
9421 G 3.5 42.6 - - - -
123B ALA 3.2 7.2 - - - +
124B HIS* 3.5 19.5 - - + -
136B ARG* 3.8 27.4 - - + -
137B LEU* 1.3 90.9 - - - +
139B CYS* 1.3 63.4 + - - +
172B MET* 4.2 2.8 - - - +
212B VAL* 2.8 20.4 - - - +
213B ARG* 3.4 30.3 - - - +
214B LYS* 2.9 54.6 + - + +
216B LYS* 5.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLU* 2.7 25.2 - - - +
123B ALA* 2.6 36.4 + - + +
138B PHE* 1.3 78.4 - - - +
140B VAL* 1.3 73.0 + - - +
168B MET* 3.5 31.2 - - - -
172B MET* 3.6 25.1 - - + -
210B VAL* 4.3 11.2 - - - -
211B PHE 4.0 9.2 - - - -
212B VAL* 4.2 0.9 - - - +
213B ARG* 3.6 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET* 6.0 3.6 - - + -
120B MET* 5.1 1.8 - - + -
121B ILE 3.6 4.9 - - - -
122B GLU* 3.3 19.7 - - - +
139B CYS* 1.3 83.2 - - - +
141B GLY* 1.3 64.1 + - - +
142B PHE* 3.6 25.4 - - + -
168B MET* 5.7 0.4 - - - -
209B ASP* 5.3 1.8 - - + -
210B VAL* 3.1 26.9 - - - +
211B PHE* 3.3 37.7 + - + +
213B ARG* 4.1 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B MET* 3.6 0.5 - - - -
121B ILE* 2.9 41.8 + - - -
140B VAL* 1.3 80.0 - - - +
142B PHE* 1.3 77.1 + - - -
168B MET* 5.8 2.9 - - - -
207B LEU* 6.3 1.1 - - - -
208B HIS 4.5 7.9 - - - -
210B VAL* 4.5 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9881 C 5.3 3.1 - - - -
113B MET* 3.3 37.0 - - + -
114B VAL* 4.4 13.9 - - + -
118B GLN* 3.6 20.0 - - + +
119B THR 3.2 20.9 - - - -
120B MET* 3.6 39.3 - - + -
121B ILE* 5.5 2.9 - - - +
140B VAL* 3.6 25.1 - - + -
141B GLY* 1.3 82.0 - - - -
143B THR* 1.3 65.8 + - - +
207B LEU* 3.0 6.4 - - - +
208B HIS* 2.9 38.2 + - + +
209B ASP* 3.1 27.8 - - - +
----------------------------------------------------------
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