Contacts of the strand formed by residues 193 - 205 (chain C) in PDB entry 3BXB
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 TYR 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C HIS* 3.0 34.1 + + - -
76C ILE* 3.8 10.8 - - + -
77C PRO 4.9 1.0 + - - -
79C PHE* 5.0 1.7 - - - +
80C PHE* 3.9 18.0 - - - -
146C MET* 3.6 1.0 - - - +
147C LEU* 2.9 52.1 + - + +
154C LEU* 4.1 8.7 - - + +
190C PRO* 3.7 29.1 - - + +
191C GLY 3.0 22.9 + - - +
192C VAL* 1.3 73.7 - - - +
194C TYR* 1.3 87.6 + - - +
195C VAL* 3.9 11.6 - - + +
219C ALA* 3.7 23.1 - - + -
220C ARG 3.4 11.9 - - - +
221C TYR* 4.0 13.7 - - + -
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Residues in contact with TYR 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C THR* 4.2 5.4 - - + -
145C GLU 3.2 7.0 - - - +
146C MET* 3.4 32.9 - - + -
147C LEU 4.9 0.2 - - - +
192C VAL* 3.8 21.5 - - + +
193C TYR* 1.3 89.3 - - - +
195C VAL* 1.3 64.7 + - - +
196C ASP 4.0 0.4 - - - -
218C VAL 3.9 0.2 - - - +
219C ALA* 3.2 3.6 - - - +
220C ARG* 2.9 71.2 + - - +
222C CYS* 4.2 24.2 - - + -
141D GLU* 4.2 0.2 - - - +
142D ALA* 2.4 46.3 + - + +
143D SER* 4.6 5.8 - - - -
144D THR* 4.6 10.8 - - - -
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 5.6 0.2 - - - +
70C ILE* 4.1 24.2 - - + -
144C THR* 3.4 0.7 - - - -
145C GLU* 2.8 33.0 + - - +
147C LEU* 3.7 21.5 - - + -
193C TYR* 3.9 5.2 - - + +
194C TYR* 1.3 76.7 - - - +
196C ASP* 1.3 65.2 + - - +
197C ARG* 2.5 47.9 + - - +
217C ALA* 4.2 14.6 - - + -
218C VAL 3.7 5.4 - - - +
219C ALA* 3.9 17.3 - - + -
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Residues in contact with ASP 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C SER 3.6 4.5 - - - +
144C THR* 2.7 21.0 + - - +
194C TYR 4.0 0.4 - - - -
195C VAL* 1.3 72.7 - - - +
197C ARG* 1.3 59.9 + - - +
217C ALA* 3.6 0.2 - - - -
218C VAL* 3.0 35.0 + - + +
220C ARG* 2.4 52.4 + - - -
220D ARG* 3.9 15.7 + - - +
222D CYS* 5.8 3.8 - - - -
224D LEU* 3.7 17.3 - - + +
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Residues in contact with ARG 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C NRQ 2.8 53.2 - - + +
67C LYS* 5.7 2.6 - - - +
70C ILE* 6.3 0.4 - - - -
142C ALA* 3.4 8.7 - - - +
143C SER* 2.7 61.2 + - - +
144C THR 3.3 0.2 - - - -
145C GLU* 3.1 23.8 + - - +
158C SER* 2.8 29.5 + - - -
195C VAL* 2.5 42.3 + - - -
196C ASP* 1.3 76.0 - - - +
198C ARG* 1.3 62.4 + - - +
215C GLU* 3.7 10.5 - - - +
216C VAL 3.2 15.3 - - - +
217C ALA* 3.8 9.9 - - + -
222D CYS* 4.6 1.0 - - - -
224D LEU* 3.6 6.8 - - - +
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Residues in contact with ARG 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C NRQ 5.2 0.4 - - - -
140C TRP 6.0 1.1 - - - +
141C GLU 5.8 0.4 - - - -
142C ALA* 4.2 20.4 - - + +
197C ARG* 1.3 75.5 - - - +
199C LEU* 1.3 61.8 + - - +
200C GLU* 3.2 39.8 + - + +
214C HIS* 3.9 1.2 - - - +
215C GLU* 3.1 4.8 - - - +
216C VAL* 2.9 45.1 + - + +
222D CYS* 3.0 43.5 + - - +
224D LEU* 2.6 33.5 + - + +
225D PRO 3.6 9.6 + - - -
226D SER* 4.1 10.7 - - - -
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ALA* 3.7 36.3 - - + +
60C THR* 4.3 3.6 - - + +
63C NRQ 3.6 52.6 + - + +
140C TRP* 4.2 31.9 + - + +
141C GLU 5.6 1.8 + - - -
142C ALA* 5.6 1.4 - - - +
160C MET* 5.7 0.4 - - + -
198C ARG* 1.3 75.8 - - - +
200C GLU* 1.3 69.6 + - - +
201C ARG* 4.4 1.1 + - - +
213C GLN* 3.9 29.2 - - + +
214C HIS 3.3 8.3 - - - +
215C GLU* 4.1 9.6 - - + +
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Residues in contact with GLU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C TRP 5.8 1.3 - - - +
198C ARG* 3.2 34.0 + - + +
199C LEU* 1.3 78.4 - - - +
201C ARG* 1.3 59.7 + - - +
202C ILE* 3.3 10.5 + - + +
213C GLN* 3.3 6.7 - - - +
214C HIS* 2.5 52.8 + - + +
225D PRO 4.7 0.9 - - - +
226D SER* 2.9 21.8 + - - -
227D LYS* 3.3 22.1 + - - +
228D LEU* 3.7 25.3 - - + +
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Residues in contact with ARG 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C PHE* 3.4 34.4 - - - +
56C ASP* 3.2 36.2 + - - +
59C ALA* 6.1 0.4 - - - +
139C GLY* 5.8 5.4 - - - -
199C LEU* 5.0 0.8 - - - +
200C GLU* 1.3 69.6 - - - +
202C ILE* 1.3 61.5 + - - +
203C LYS 3.9 13.7 - - - +
204C GLU* 2.7 50.3 + - + +
208C GLU* 3.5 19.6 + - - +
211C VAL* 3.7 28.1 - - - +
212C GLU 4.2 2.0 - - - -
213C GLN* 4.5 6.6 + - + -
228D LEU* 3.3 21.1 - - - +
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Residues in contact with ILE 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C THR* 5.8 0.9 - - + +
200C GLU* 3.3 12.1 + - + +
201C ARG* 1.3 75.3 - - - +
203C LYS* 1.3 72.3 + - + +
212C GLU* 3.0 34.9 + - - +
213C GLN 4.4 0.4 - - - -
214C HIS* 3.6 31.6 - - + +
227D LYS* 3.7 39.9 - - + +
228D LEU* 4.6 14.1 - - + +
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Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C ARG* 3.7 5.1 - - - -
202C ILE* 1.3 89.4 - - + +
204C GLU* 1.3 68.8 + - - +
210C TYR* 5.4 8.3 - - + -
211C VAL* 3.6 1.2 - - - -
212C GLU* 2.8 46.8 + - + +
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Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C ARG* 2.7 43.0 + - + +
203C LYS* 1.3 82.4 - - - +
205C ALA* 1.3 61.2 + - - +
207C LYS* 5.7 0.5 - - - -
208C GLU* 3.5 23.6 + - - +
210C TYR* 3.3 14.8 - - - +
211C VAL* 4.6 1.8 - - + -
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Residues in contact with ALA 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C GLU* 1.3 75.2 - - - +
206C ASP* 1.3 79.2 + - - +
207C LYS 3.4 2.0 - - - -
208C GLU 3.0 13.8 + - - -
210C TYR* 3.1 39.9 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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