Contacts of the strand formed by residues 210 - 216 (chain F) in PDB entry 5LN3
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 210 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F VAL* 4.8 8.5 - - + -
48F ALA 3.8 5.6 - - - +
49F LEU* 4.7 4.3 - - + +
50F LYS* 4.1 6.4 - - - -
192F LEU* 4.8 17.7 - - + -
195F LEU* 4.5 18.8 - - + -
205F LEU* 5.8 4.7 - - + -
206F THR 3.3 24.2 + - - +
207F THR* 3.7 17.4 - - - +
208F LYS 3.5 0.4 - - - -
209F ASN* 1.4 82.7 - - + +
211F SER* 1.4 62.3 + - - +
212F ILE* 5.0 5.4 - - + -
226F ASP 4.4 5.9 + - - -
229F VAL* 3.9 25.3 - - + +
233F LEU* 5.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F LEU 3.8 1.0 - - - +
47F VAL* 3.6 4.0 - - - +
48F ALA* 2.8 47.7 + - - +
50F LYS* 4.0 30.4 - - - +
63F ILE* 3.6 24.0 - - - +
210F VAL* 1.4 78.9 - - - +
212F ILE* 1.3 63.0 + - - +
223F ILE* 6.1 0.2 - - - -
224F TYR 3.9 13.2 - - - -
225F ASP* 5.3 1.6 - - - -
229F VAL* 4.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F VAL* 3.8 23.8 - - + -
46F LEU 3.9 3.8 - - - +
47F VAL* 4.5 16.2 - - + -
63F ILE* 4.8 1.3 - - - -
188F VAL* 4.1 32.3 - - + -
192F LEU* 6.6 0.2 - - + -
210F VAL* 5.0 5.6 - - + -
211F SER* 1.3 77.8 - - - +
213F GLY* 1.3 59.9 + - - +
214F ILE* 4.9 1.6 - - + -
223F ILE* 3.8 3.5 - - - +
224F TYR* 2.8 52.8 + - + +
229F VAL* 3.8 35.9 - - + +
232F PHE* 5.7 5.4 - - + -
233F LEU* 4.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F VAL* 3.6 1.9 - - - +
46F LEU* 3.3 34.0 + - - +
63F ILE* 4.8 7.2 - - - +
212F ILE* 1.3 77.5 - - - +
214F ILE* 1.4 62.4 + - - +
221F PHE* 6.5 0.4 - - - -
222F THR 3.5 13.0 - - - -
223F ILE* 4.5 8.1 - - - -
224F TYR* 4.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F HIS* 5.4 1.3 - - + +
44F ALA 3.7 8.5 - - - +
45F VAL* 4.1 18.2 - - + -
184F LEU* 5.0 24.7 - - + +
188F VAL* 4.8 12.3 - - + -
212F ILE* 4.9 1.1 - - + -
213F GLY* 1.4 75.3 - - - +
215F VAL* 1.4 73.2 + - - +
216F GLY* 5.3 0.2 - - - -
219F LEU* 3.9 25.1 - - + -
220F GLU 3.1 14.4 - - - +
221F PHE* 4.3 2.1 - - - -
222F THR* 3.4 17.9 + - - +
224F TYR* 3.7 31.1 - - + +
232F PHE* 5.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F HIS* 3.8 1.4 + - - -
44F ALA* 3.1 42.4 + - + +
46F LEU* 6.4 0.4 - - + -
69F HIS* 4.6 10.1 - - - +
70F ILE* 6.4 0.2 - - - -
135F ALA* 5.0 7.2 - - + -
136F GLY* 4.8 21.3 - - - +
137F TYR* 3.9 19.3 - - + -
142F PRO* 5.5 2.5 - - + -
214F ILE* 1.4 80.5 - - - +
216F GLY* 1.4 60.4 + - - +
219F LEU* 3.7 19.7 - - - +
220F GLU* 3.7 19.3 - - - +
221F PHE* 4.6 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F THR 3.7 8.1 - - - -
43F HIS* 3.2 19.7 - - - -
137F TYR* 3.6 18.8 - - - +
142F PRO* 5.6 1.3 - - - -
215F VAL* 1.4 78.8 - - - +
217F LYS* 1.4 63.4 + - - +
218F ASP 3.4 2.5 - - - -
219F LEU* 3.2 23.6 - - - +
----------------------------------------------------------
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