Contacts of the strand formed by residues 214 - 221 (chain C) in PDB entry 2I7C
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 LYS 214 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C LYS* 1.3 82.6 - - - +
215C VAL* 1.3 69.5 + - - +
216C GLU* 3.3 29.4 - - + -
234C CYS 3.7 0.5 - - - +
235C CYS* 3.7 0.5 - - - -
236C SER* 2.9 35.6 + - - +
238C THR 3.4 19.1 - - - +
239C ASP* 3.9 22.6 + - - +
240C THR 5.3 1.3 - - - -
241C GLY* 3.7 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ILE* 3.9 22.4 - - + +
208C ALA* 3.6 41.5 - - + +
209C LYS* 3.8 18.8 - - + +
212C PHE* 3.8 11.7 - - + +
213C LYS 4.4 0.2 - - - -
214C LYS* 1.3 83.5 - - - +
216C GLU* 1.3 68.6 + - - +
233C LEU* 3.8 27.8 - - + -
234C CYS 3.3 6.1 - - - +
235C CYS* 4.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ILE* 5.5 1.6 - - - -
214C LYS* 3.3 37.8 - - + +
215C VAL* 1.3 81.2 - - - +
217C TYR* 1.3 63.9 + - - +
233C LEU* 3.9 7.6 - - - +
234C CYS* 2.9 33.4 + - + +
236C SER* 4.6 1.2 + - - -
240C THR 4.6 1.7 - - - +
241C GLY* 3.4 6.4 - - - -
242C LEU* 2.7 32.7 + - - +
243C THR* 3.3 25.3 + - + +
269C PHE* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C CYS* 2.9 29.4 + - + -
192C GLU 2.9 26.9 + - - -
194C LEU* 4.0 12.9 + - + -
201C ILE* 3.3 34.5 - - + +
205C ILE* 4.3 17.5 - - + -
216C GLU* 1.3 79.0 - - - +
218C ALA* 1.3 70.3 + - - +
219C ASN* 5.0 1.0 + - - -
231C GLY* 3.3 12.8 - - - -
232C ILE 3.3 13.2 - - - -
233C LEU* 4.5 5.6 - - - -
269C PHE* 3.5 15.4 - - - +
271C LEU* 3.6 33.5 - - + +
275C LEU* 4.0 27.6 - - + -
279C ILE* 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C VAL* 5.7 0.7 - - + -
217C TYR* 1.3 79.0 - - - +
219C ASN* 1.3 60.3 + - - +
231C GLY* 3.1 5.2 - - - -
232C ILE* 2.8 51.3 + - + -
268C ALA* 3.3 24.7 - - + +
269C PHE* 3.8 27.6 - - + -
271C LEU* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B SER* 4.3 14.5 + - - -
66C MET* 5.2 0.9 - - - +
194C LEU* 3.7 30.6 + - + +
217C TYR* 5.0 1.5 + - + -
218C ALA* 1.3 75.1 - - - +
220C ILE* 1.3 68.3 + - - +
221C SER* 4.3 0.7 + - - +
229C CYS* 3.5 31.8 - - - +
230C ILE 3.5 13.0 - - - +
231C GLY* 4.2 1.8 + - - -
259C TYR* 4.5 3.1 + - - -
268C ALA* 2.9 32.0 + - - +
271C LEU* 4.4 6.5 - - + -
272C PRO* 5.9 1.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA* 3.6 26.9 - - + +
63C TYR* 4.1 20.4 - - + +
66C MET* 3.8 21.1 - - + -
67C MET* 4.4 1.8 - - + -
219C ASN* 1.3 79.8 - - - +
221C SER* 1.3 74.2 + - - +
222C ILE* 3.5 4.8 + - + +
229C CYS* 3.1 29.4 - - - +
230C ILE* 2.8 35.5 + - + +
231C GLY 5.0 0.4 - - - -
232C ILE* 3.6 32.8 - - + -
259C TYR* 3.8 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 5.1 0.4 - - - +
195B TRP* 2.9 39.7 + - - -
219B ASN* 4.3 13.2 + - - -
227B CYS 5.3 0.3 + - - -
229B CYS* 4.2 12.4 - - - +
272B PRO* 5.7 2.9 - - - -
62C ALA* 3.5 3.1 - - - +
219C ASN* 4.3 1.7 + - - +
220C ILE* 1.3 69.9 - - - +
222C ILE* 1.3 62.6 + - - +
228C GLY 3.7 8.3 + - - -
229C CYS* 4.6 2.2 - - - -
259C TYR* 3.0 29.3 + - - -
----------------------------------------------------------
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