Contacts of the strand formed by residues 209 - 219 (chain F) in PDB entry 1LE9
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 VAL 209 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F PHE* 4.4 1.8 - - - -
100F ASN* 4.1 24.8 + - + +
107F HIS* 2.9 26.5 + - - -
109F HIS* 5.0 0.4 - - - -
206F ASP* 3.5 15.7 + - + +
207F LEU 3.6 0.8 - - - -
208F SER* 1.3 91.5 - - - +
210F VAL* 1.3 65.5 + - - +
236F ALA* 4.7 0.2 - - + -
237F ILE 3.2 18.4 - - - +
238F TYR* 3.4 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 210 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F PHE* 4.6 6.9 - - + -
97F LEU* 3.4 32.8 - - + -
98F VAL 3.1 19.5 - - - +
100F ASN 5.0 1.6 - - - +
107F HIS* 3.7 15.9 - - + +
109F HIS* 4.9 7.0 - - - +
139F ILE* 4.7 21.1 - - + -
209F VAL* 1.3 75.0 - - - +
211F ARG* 1.3 80.5 + - - +
212F LEU* 5.9 5.2 - - + -
237F ILE* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LEU* 3.6 3.4 - - - -
98F VAL* 2.8 46.6 + - + +
99F THR 2.5 24.7 + - - -
100F ASN* 2.9 44.6 - - + +
101F GLY 3.1 13.1 + - - +
104F ILE* 3.0 36.9 - - - +
210F VAL* 1.3 94.0 - - - +
212F LEU* 1.3 63.7 + - - +
233F VAL* 5.1 11.3 - - + +
234F SER* 4.2 11.4 - - - +
235F ASP 3.4 16.6 + - - -
236F ALA* 3.8 12.1 - - - +
237F ILE* 5.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ILE* 4.9 0.2 - - + -
48F PRO* 4.2 12.6 - - + -
67F LEU* 5.2 10.3 - - + -
80F PRO* 4.0 22.2 - - + -
95F VAL* 4.2 12.6 - - + -
96F GLN 3.8 2.9 - - - -
97F LEU* 5.1 1.6 - - + +
98F VAL* 3.9 1.0 - - - +
111F LEU* 4.8 9.6 - - + -
137F LEU* 4.7 16.6 - - + -
139F ILE* 6.2 2.2 - - + -
210F VAL* 5.9 4.7 - - + -
211F ARG* 1.3 78.2 - - - +
213F MET* 1.3 59.1 + - - +
214F PHE* 3.4 28.5 - - + -
233F VAL* 3.2 7.3 - - - +
234F SER* 2.6 51.1 + - - +
237F ILE* 5.3 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F ILE* 3.4 13.6 - - + +
95F VAL* 3.5 11.8 - - - +
96F GLN* 2.9 61.2 + - + +
98F VAL* 3.3 15.9 - - + -
163F TYR* 5.4 1.6 - - + +
164F ASN* 3.3 27.1 - - + +
168F LEU* 3.1 27.6 - - + -
212F LEU* 1.3 72.2 - - - +
214F PHE* 1.3 62.1 + - - +
215F THR* 3.4 20.7 + - - +
231F PRO* 4.2 12.3 - - + -
232F VAL 4.4 2.5 - - - -
233F VAL* 4.5 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 214 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 3.4 16.3 - - + +
43F GLN 3.4 17.9 - - - +
44F ILE* 3.9 13.7 - - + -
80F PRO* 4.4 18.2 - - + -
82F VAL* 3.5 39.9 - - + -
93F VAL* 4.2 9.6 - - + -
94F ILE 4.0 3.4 - - - -
95F VAL* 4.6 8.5 - - + -
134F PHE* 4.3 20.9 - + - -
212F LEU* 3.4 37.0 - - + -
213F MET* 1.3 68.7 - - - +
215F THR* 1.3 58.4 + - - +
231F PRO* 3.1 4.7 - - - +
232F VAL* 2.8 43.7 + - + +
234F SER* 3.6 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 3.4 7.4 - - - +
92F LYS 3.9 0.3 - - - +
93F VAL* 3.2 2.1 - - - -
94F ILE* 2.8 48.2 + - + +
163F TYR* 6.0 1.6 - - + -
164F ASN* 5.3 10.3 - - - +
165F PRO* 5.5 1.1 - - + -
213F MET* 3.7 14.6 + - - +
214F PHE* 1.3 71.1 - - - +
216F ALA* 1.3 63.0 + - - +
217F PHE* 3.9 25.4 - - + -
228F ARG* 5.1 4.5 - - + -
229F LEU 3.9 9.6 - - - +
231F PRO* 3.0 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 3.2 21.8 - - + +
84F ILE* 4.8 6.3 - - + -
91F ALA* 5.6 0.9 - - + -
92F LYS 3.5 3.1 - - - -
93F VAL* 3.3 23.1 - - + -
215F THR* 1.3 73.8 - - - +
217F PHE* 1.3 64.6 + - - +
218F LEU* 5.1 0.4 - - + -
227F ARG 3.3 1.0 - - - +
228F ARG 3.9 0.2 - - - -
229F LEU* 2.9 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ALA* 3.6 1.6 - - - -
92F LYS* 2.7 62.8 + - - +
94F ILE* 4.4 3.8 - - + -
162F GLY 3.4 23.8 - - - -
163F TYR* 3.2 24.7 - + - -
164F ASN 5.4 1.3 - - - -
165F PRO* 5.9 0.7 - - + -
177F GLN* 4.6 10.5 - - - -
215F THR* 3.9 22.0 - - + -
216F ALA* 1.3 75.9 - - - +
218F LEU* 1.3 63.9 + - - +
225F PHE* 2.8 33.5 - - + +
226F THR* 3.5 28.0 - - - -
227F ARG 3.3 4.9 - - - -
228F ARG* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F GLY 3.2 31.2 - - - +
40F PRO* 3.5 21.8 - - + +
84F ILE* 4.6 2.5 - - + -
88F VAL* 3.1 43.5 - - + -
91F ALA* 4.1 6.1 - - + -
217F PHE* 1.3 75.9 - - - +
219F PRO* 1.3 76.9 - - - +
225F PHE* 4.0 1.6 - - - -
226F THR 3.6 3.8 + - - -
227F ARG* 3.3 30.0 + - + +
229F LEU* 3.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 219 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F VAL* 4.2 8.1 - - + +
90F PRO* 3.1 35.4 - - + +
218F LEU* 1.3 98.9 - - + +
220F ASP* 1.3 62.8 + - - +
223F GLY* 3.9 12.3 - - - +
224F SER 2.8 14.1 - - - +
225F PHE* 3.1 30.7 - - + -
227F ARG* 4.8 3.3 - - - +
----------------------------------------------------------
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