Contacts of the helix formed by residues 199 - 218 (chain C) in PDB entry 2B5F
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 PRO 199 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 3.1 37.9 - - + +
89C VAL* 4.0 15.3 - - + -
90C TYR* 3.5 40.2 - - + +
197C LEU 3.7 5.8 - - - +
198C ALA* 1.3 80.8 - - + +
200C LEU* 1.3 52.6 + - - +
201C PRO 2.5 20.5 - - - -
202C ILE* 2.6 19.0 + - + +
203C GLY 2.7 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 3.7 10.1 - - + -
196A ILE* 5.5 10.1 - - + -
200A LEU* 3.7 25.1 - - + -
86C PHE* 3.4 32.6 - - + -
199C PRO* 1.3 75.7 - - - +
201C PRO* 1.4 68.9 - - + +
203C GLY 3.8 1.3 - - - +
204C PHE* 3.1 53.9 + - + +
200D LEU* 3.5 31.4 - - + -
204D PHE* 5.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 3.6 19.5 - - + -
87A VAL* 4.2 5.5 - - + +
90A TYR* 3.9 44.4 - - + -
196A ILE* 5.8 5.4 - - + -
178C THR* 3.8 20.8 - - + +
182C ALA* 5.1 2.7 - - + -
198C ALA* 4.0 16.6 - - + +
199C PRO 2.5 8.5 - - - +
200C LEU* 1.4 85.4 - - + +
202C ILE* 1.3 54.7 + - - +
204C PHE* 3.4 4.0 + - - +
205C ALA* 2.6 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE* 3.1 29.6 - - + -
86C PHE* 5.9 0.2 - - - -
89C VAL* 4.6 15.7 - - + -
175C LEU* 3.7 13.2 - - + -
178C THR* 4.6 10.3 - - + -
179C VAL* 3.7 31.4 - - + +
182C ALA* 4.6 10.1 - - + -
197C LEU* 4.0 20.2 - - + -
198C ALA 4.7 5.8 - - - +
199C PRO* 2.6 13.4 + - + +
201C PRO* 1.3 72.2 - - - +
203C GLY* 1.3 76.9 - - - +
204C PHE 2.5 2.0 + - - -
205C ALA* 2.7 12.2 + - - +
206C VAL* 2.8 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TRP* 6.4 0.9 - - - -
82C GLY* 3.1 34.9 - - - -
83C GLY* 5.3 0.2 - - - -
86C PHE* 3.5 21.9 - - - +
199C PRO 2.7 12.2 + - - -
200C LEU* 4.0 2.7 - - - -
202C ILE* 1.3 86.8 - - - +
204C PHE* 1.3 60.8 + - - +
207C PHE* 3.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 4.0 27.8 - + - -
83A GLY* 4.3 17.7 - - - -
86A PHE* 3.9 24.9 - + + -
87A VAL* 4.0 10.5 - - + -
200A LEU* 5.4 8.5 - - + -
204A PHE* 5.6 2.5 - + - -
79C TRP* 3.9 30.3 - + - -
200C LEU* 3.1 41.3 + - + +
201C PRO 3.4 4.3 - - - +
202C ILE 2.5 4.4 + - - -
203C GLY* 1.3 71.4 - - - +
205C ALA* 1.3 58.0 + - - +
206C VAL 2.9 5.7 + - - -
207C PHE* 3.1 19.3 + + - +
208C MET* 2.8 39.1 + - + +
204D PHE* 5.4 3.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 4.1 11.4 - - + +
174C VAL* 4.3 6.0 - - + +
175C LEU* 4.5 13.4 - - - +
178C THR* 3.4 33.7 - - + +
201C PRO 2.6 20.7 + - - +
202C ILE* 2.7 12.7 + - + -
204C PHE* 1.3 70.3 - - - +
206C VAL* 1.4 56.9 + - - +
208C MET* 4.2 3.5 - - - +
209C VAL* 3.3 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PHE* 5.7 1.3 - - + -
81C PHE* 3.8 8.7 - - + +
82C GLY* 3.8 17.7 - - - +
85C ILE* 4.0 15.7 - - + -
175C LEU* 3.8 20.4 - - + -
202C ILE* 2.8 33.8 + - + +
203C GLY 3.8 2.2 - - - +
205C ALA* 1.4 75.7 - - - +
207C PHE* 1.3 67.1 + - - +
208C MET 3.2 0.2 - - - -
209C VAL* 3.3 2.8 + - - +
210C HIS* 2.9 51.6 + - + +
221C ILE* 4.6 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 4.3 16.4 - + - -
75C LEU* 3.9 18.8 - - + -
78C ALA* 3.6 40.4 - - + -
79C TRP* 3.3 59.9 - + + -
82C GLY* 3.7 7.8 - - - -
203C GLY 3.2 11.9 + - - +
204C PHE* 3.4 16.6 - + - +
206C VAL* 1.3 79.2 - - - +
208C MET* 1.3 84.9 + - + +
210C HIS* 3.1 11.6 + - - +
211C LEU* 3.1 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 3.9 11.0 - - + +
79A TRP 3.6 22.7 - - - +
80A ALA* 3.9 11.0 - - - +
83A GLY* 3.6 27.1 - - - +
84A MET* 3.6 29.8 - - + -
87A VAL* 4.4 3.6 - - + -
174C VAL* 5.7 0.7 - - + -
204C PHE* 2.8 28.7 + - + +
205C ALA* 4.6 4.7 - - - +
207C PHE* 1.3 110.8 - - + +
209C VAL* 1.3 65.2 + - + +
211C LEU* 3.0 32.8 + - + +
212C ALA 3.4 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 4.4 13.7 - - + -
171C GLY* 3.6 40.8 - - - +
174C VAL* 3.8 20.0 - - + -
175C LEU 4.9 0.4 - - - +
205C ALA 3.3 18.4 + - - +
206C VAL 3.3 7.9 + - - +
208C MET* 1.3 76.1 - - + +
210C HIS* 1.4 57.5 + - - +
212C ALA 3.4 1.2 + - - -
213C THR* 2.9 43.8 + - - +
219C THR* 4.3 3.4 - - + -
221C ILE* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ALA* 3.8 17.9 - - + -
81C PHE* 3.1 57.3 - + + +
206C VAL* 2.9 44.3 + - + +
207C PHE 3.1 6.9 + - - +
209C VAL* 1.4 76.8 - - - +
211C LEU* 1.3 62.1 + - - +
214C ILE* 3.0 41.5 + - + +
218C GLY 4.4 1.0 + - - -
219C THR* 3.1 47.6 + - + +
220C GLY 4.4 6.5 + - - -
221C ILE* 4.6 3.8 - - + +
225C ARG* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 5.8 0.2 - - + -
58A THR* 2.7 29.1 + - + +
61A GLY* 6.1 0.3 - - - -
72A VAL* 4.0 31.4 - - + +
76A GLY 4.0 16.6 - - - +
79A TRP* 4.2 2.0 - - + -
80A ALA* 4.1 12.1 - - + +
75C LEU* 3.9 21.5 - - + -
78C ALA* 3.8 20.2 - - + -
207C PHE* 3.1 22.5 + - + +
208C MET* 3.0 38.1 + - + +
210C HIS* 1.3 78.4 - - - +
212C ALA* 1.3 56.9 + - - +
214C ILE* 5.3 0.2 - - - +
215C PRO* 4.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 4.6 6.1 + - + -
54A ILE* 3.8 30.5 - - + +
57A ALA* 3.7 26.4 - - + +
58A THR* 2.9 13.3 + - - +
141A MET* 5.8 0.2 - - - +
208C MET 3.4 6.5 + - - +
209C VAL 3.4 7.3 + - - +
210C HIS 3.2 0.4 - - - -
211C LEU* 1.3 78.2 - - - +
213C THR* 1.3 63.8 + - - +
214C ILE 3.7 0.2 - - - -
215C PRO* 3.8 9.4 - - - +
216C ILE* 4.7 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 4.8 7.7 + - - -
54A ILE* 5.9 0.2 - - - +
167C ALA* 4.5 22.8 + - + +
168C GLU* 4.1 6.3 - - - +
171C GLY* 5.1 0.9 - - - -
209C VAL* 2.9 30.9 + - + +
212C ALA* 1.3 80.0 - - - +
214C ILE* 1.3 66.8 + - - +
215C PRO* 3.2 3.9 - - - -
216C ILE* 3.3 6.5 + - + +
217C THR* 2.9 48.8 + - + +
218C GLY 3.3 1.6 + - - -
219C THR* 3.2 15.0 - - + -
220C GLY 4.6 0.4 - - - +
221C ILE* 5.6 0.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
72A VAL* 5.8 4.5 - - + -
74C LEU* 4.0 48.9 - - + +
77C ILE* 4.2 22.0 - - + -
78C ALA* 4.2 4.5 - - + +
210C HIS* 3.0 30.9 + - + +
211C LEU* 5.3 1.3 - - - +
213C THR* 1.3 76.3 - - - +
215C PRO* 1.3 66.8 - - + +
218C GLY* 2.7 35.5 + - - +
219C THR* 2.8 26.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
61A GLY* 3.9 31.6 - - - +
72A VAL* 6.2 3.1 - - + -
74C LEU* 5.7 5.6 - - + -
156C ALA* 3.3 20.8 - - - +
159C TYR* 4.2 15.8 - - - +
211C LEU 4.4 7.2 - - - +
212C ALA 3.8 14.4 - - - +
213C THR 3.4 4.3 - - - -
214C ILE* 1.3 99.9 - - + +
216C ILE* 1.3 60.4 + - + +
218C GLY 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 4.9 4.9 - - - +
140A PHE* 4.8 2.7 - - + -
141A MET* 3.4 28.7 - - + -
155C VAL* 4.0 3.6 - - + +
156C ALA* 3.4 25.7 + - - +
159C TYR* 3.5 45.8 - - + +
163C THR* 4.3 10.8 - - + -
164C ALA* 4.1 15.3 - - + -
167C ALA* 4.3 19.5 - - + -
212C ALA 4.7 11.7 - - - +
213C THR* 3.3 5.8 + - + +
215C PRO* 1.3 78.9 - - + +
217C THR* 1.3 74.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ASN* 3.1 17.2 + - - -
154C SER 3.8 18.8 + - - +
164C ALA* 4.0 26.5 - - + +
167C ALA* 4.8 1.3 - - + -
168C GLU* 2.5 31.7 + - + +
213C THR* 2.9 14.8 + - + +
216C ILE* 1.3 93.9 - - + +
218C GLY* 1.3 55.6 + - - +
219C THR* 2.6 23.1 + - - -
245C PHE* 3.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE* 5.5 2.3 - - - -
153C ASN* 4.4 1.6 + - - -
210C HIS* 4.4 3.5 + - - -
214C ILE* 2.7 39.5 + - - +
215C PRO 4.7 0.2 + - - -
216C ILE 3.8 0.4 - - - -
217C THR* 1.3 71.7 - - - +
219C THR* 1.3 72.4 + - - +
225C ARG* 4.4 9.7 + - - -
----------------------------------------------------------
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