Contacts of the strand formed by residues 213 - 224 (chain C) in PDB entry 4BEI
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 ILE 213 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C THR* 3.9 27.4 - - + +
206C ALA 3.7 2.7 - - - -
207C VAL* 4.5 4.9 - - + +
211C GLY 3.5 6.5 + - - +
212C LEU* 1.3 77.6 - - - +
214C ILE* 1.3 59.3 + - - +
77D TRP* 3.2 9.5 + - - -
79D SER* 2.7 48.6 + - - +
80D ILE 4.6 4.5 - - - +
81D LYS* 3.9 23.8 - - + -
87D TYR* 3.9 37.5 - - + -
88D PHE 5.3 0.2 - - - +
132D SER* 5.3 5.4 - - - -
134D GLN* 2.9 18.3 + - - +
1272D O4B 4.6 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C THR* 3.2 4.2 - - - -
206C ALA* 2.7 49.4 + - + +
212C LEU* 4.3 15.5 - - + -
213C ILE* 1.3 73.6 - - - +
215C PRO* 1.3 81.4 - - + +
216C VAL* 3.3 0.9 + - - +
236C ILE* 4.7 10.1 - - + -
242C TYR* 3.9 41.1 - - + +
247C TYR* 3.8 31.0 - - + -
77D TRP* 3.6 25.8 - - + +
101D GLN* 4.9 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C MET 4.0 5.2 - - - +
205C THR* 4.6 1.6 - - + -
213C ILE 3.4 9.2 - - - +
214C ILE* 1.3 94.9 - - + +
216C VAL* 1.3 59.8 + - - +
217C ASN 5.1 2.5 - - - +
218C ALA* 5.7 1.1 - - - +
236C ILE* 5.6 0.3 - - - +
77D TRP* 3.5 33.4 - - + -
78D LEU 4.7 2.9 - - - +
79D SER* 3.9 11.2 - - - +
89D PRO* 4.0 28.0 - - + -
91D LYS* 6.3 1.3 - - + -
101D GLN* 3.9 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C PHE* 5.6 0.7 - - + -
204C MET* 2.9 41.8 + - + +
205C THR 3.7 2.9 - - - +
206C ALA* 3.6 24.7 - - + +
214C ILE 3.6 13.9 - - - +
215C PRO* 1.3 74.9 - - - +
217C ASN* 1.3 60.4 + - - +
234C ARG* 2.9 39.3 + - + +
235C GLY 4.6 5.2 - - - +
236C ILE* 4.0 34.8 - - + -
249C ILE* 4.9 4.5 - - + -
97D ASP* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PHE* 3.7 14.6 - - - -
203C TRP* 3.5 3.8 - - - +
204C MET* 2.9 49.2 + - + +
215C PRO* 5.4 0.7 - - - -
216C VAL* 1.3 78.6 - - - +
218C ALA* 1.3 91.4 + - - +
220C GLU* 3.1 15.8 + - - +
232C LYS* 3.0 37.8 - - - +
234C ARG* 3.6 15.3 - - - +
89D PRO* 3.6 5.7 - - - +
97D ASP* 3.3 7.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
202C PHE 3.4 3.6 - - - +
215C PRO* 5.7 1.9 - - - +
217C ASN* 1.3 92.4 + - - +
219C ARG* 1.3 66.7 + - - +
220C GLU* 3.2 5.0 + - - +
89D PRO* 4.2 7.6 - - - -
91D LYS* 3.7 23.1 - - + +
93D VAL* 4.0 21.5 - - + +
97D ASP* 2.6 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLU* 3.8 25.0 + - - +
202C PHE 3.5 5.4 - - - -
203C TRP* 3.7 29.4 - - + +
218C ALA* 1.3 73.9 - - - +
220C GLU* 1.3 58.3 + - - +
221C LYS* 4.3 1.2 + - - +
88D PHE* 3.5 30.1 - - - -
89D PRO* 3.2 19.4 + - + +
90D ALA 2.9 24.2 + - - -
91D LYS 3.3 8.5 + - - +
92D ALA* 3.6 14.9 - - + +
93D VAL 3.1 26.3 + - - +
118D PHE* 3.6 11.3 - - - +
119D TRP* 2.9 36.2 + - - +
121D PRO* 3.8 19.0 - - - +
124D MET* 5.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C VAL 3.9 0.3 - - - +
201C GLU* 3.2 4.4 - - - +
202C PHE* 2.8 48.9 + - + +
217C ASN* 3.1 16.7 - - - +
218C ALA 3.7 9.9 - - - +
219C ARG* 1.3 75.2 - - - +
221C LYS* 1.3 62.8 + - - +
222C TRP* 2.7 32.6 + - + +
230C TYR* 2.5 24.7 + - - -
232C LYS* 3.2 11.7 + - - -
93D VAL* 4.0 12.3 - - + -
95D GLY 3.9 13.9 - - - +
96D VAL* 4.2 0.2 - - - -
97D ASP 2.8 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C VAL 3.5 4.5 - - - -
201C GLU* 4.0 15.1 + - - +
219C ARG 4.3 1.7 + - - +
220C GLU* 1.3 74.3 - - - +
222C TRP* 1.3 75.4 + - - +
256C ILE* 3.8 27.4 - - + -
93D VAL 4.6 5.3 + - - +
94D VAL* 4.8 8.6 + - - +
121D PRO* 6.1 0.6 - - - +
123D TYR* 3.9 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C LEU* 5.9 0.4 - - + -
198C ALA 3.5 1.7 - - - +
199C ASN* 3.4 5.1 - - - +
200C VAL* 2.8 50.3 + - + +
202C PHE* 5.2 6.7 - - + -
220C GLU* 2.7 38.1 + - + +
221C LYS* 1.3 87.5 - - - +
223C VAL* 1.3 73.2 + - - +
224C ILE* 4.2 13.2 - - + -
230C TYR* 3.6 42.9 - + - -
256C ILE* 5.2 0.9 - - - +
94D VAL 5.1 3.4 - - - -
95D GLY* 4.0 12.6 - - - -
96D VAL* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C GLU* 3.6 39.3 - - + +
198C ALA 3.6 3.6 - - - +
199C ASN* 3.3 18.8 - - - +
222C TRP* 1.3 82.4 - - - +
224C ILE* 1.3 64.1 + - - +
225C ALA* 4.0 2.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LEU* 4.4 10.1 - - + -
190C LEU* 4.2 17.9 - - + +
192C ASN* 2.8 33.2 + - + +
197C GLU* 4.4 1.8 - - - -
198C ALA* 2.9 30.2 + - + +
200C VAL* 4.1 22.0 - - + -
222C TRP* 4.2 13.7 - - + -
223C VAL* 1.3 76.1 - - - +
225C ALA* 1.3 65.8 + - - +
228C ASP* 3.6 31.6 - - + +
229C THR 4.4 1.8 - - - +
230C TYR* 4.1 26.9 - - + +
----------------------------------------------------------
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