Contacts of the strand formed by residues 197 - 205 (chain C) in PDB entry 3BPL
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 197 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C TYR* 4.8 9.4 - + - -
168C ARG 3.5 13.5 - - - -
169C THR* 3.7 22.0 - - + +
188C LEU* 4.1 22.7 - - + -
190C SER 4.1 4.6 + - - -
191C VAL* 3.6 25.7 - - + -
192C ASP* 3.0 48.8 + - + +
195C LYS* 3.6 12.8 - - + -
196C ARG* 1.3 75.3 - - - +
198C THR* 1.3 65.5 + - - +
199C PHE* 3.5 22.9 - + + -
223C HIS* 3.1 8.5 + - - +
224C TRP* 3.0 43.5 + + + +
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Residues in contact with THR 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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167C TYR* 3.2 24.9 - - - +
168C ARG* 3.1 18.0 + - - -
169C THR 6.0 0.2 - - - -
170C ASP* 4.2 9.9 + - - -
175C TRP* 3.5 25.4 - - + -
197C TYR* 1.3 73.4 - - - +
199C PHE* 1.3 65.3 + - - +
221C PRO* 3.9 17.0 - - + -
222C ILE 3.1 11.2 - - - +
223C HIS* 3.0 32.5 + - + -
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Residues in contact with PHE 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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138C LEU* 4.4 0.8 - - - +
140C LEU* 3.8 32.8 - - + -
148C LEU* 4.4 13.7 - - + -
150C LEU* 4.0 26.2 - - + -
165C VAL* 4.8 4.0 - - + -
166C GLN 3.3 5.8 - - - +
167C TYR* 3.3 33.7 - + + -
175C TRP* 4.5 1.3 - - - -
186C PHE* 4.6 5.8 - + - -
188C LEU* 3.6 31.6 - - + -
197C TYR* 3.5 29.8 - + + -
198C THR* 1.3 77.0 - - - +
200C ARG* 1.3 65.7 + - - +
220C HIS 4.3 0.3 - - - +
221C PRO* 3.4 4.6 - - - +
222C ILE* 2.9 44.1 + - + +
224C TRP* 4.6 1.1 - - + -
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Residues in contact with ARG 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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138C LEU* 4.4 2.5 - - - -
166C GLN* 2.7 67.4 + - + +
175C TRP* 4.0 40.7 - - + +
199C PHE* 1.3 78.6 - - - +
201C VAL* 1.3 64.5 + - - +
218C TRP* 3.3 50.9 - - + +
219C SER* 3.8 22.0 - - - +
221C PRO* 4.6 9.9 - - + +
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Residues in contact with VAL 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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135C PRO* 3.6 28.4 - - + +
138C LEU* 4.6 5.4 - - + +
150C LEU* 4.1 7.4 - - + -
152C TRP* 3.8 32.3 - - + -
163C HIS* 5.4 0.2 - - + -
164C LEU 3.3 8.7 - - - +
165C VAL* 3.3 34.8 - - + -
200C ARG* 1.3 81.2 - - - +
202C ARG* 1.3 64.3 + - - +
218C TRP* 3.6 4.9 - - - -
219C SER* 2.9 35.4 + - - +
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Residues in contact with ARG 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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135C PRO* 3.8 4.9 - - - -
163C HIS* 3.4 4.6 - - - +
164C LEU* 3.1 48.8 + - + +
177C GLU* 4.8 1.8 + - - -
201C VAL* 1.3 76.4 - - - +
203C SER* 1.3 62.5 + - - +
215C TRP* 3.5 45.7 - - + +
216C SER* 3.5 32.3 + - - +
217C GLU 4.1 3.6 - - - +
218C TRP* 3.6 50.4 - - + +
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Residues in contact with SER 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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132C PRO* 3.4 13.7 - - - +
133C TRP 4.9 0.2 - - - -
135C PRO* 3.1 8.4 - - - +
154C ASN* 2.8 20.4 + - - -
161C LEU* 3.9 15.0 - - - -
162C GLU 3.1 6.3 - - - -
163C HIS* 2.7 30.1 - - - -
202C ARG* 1.3 72.5 - - - +
204C ARG* 1.3 62.3 + - - +
215C TRP* 3.7 2.8 - - - -
216C SER* 3.0 33.6 + - - -
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Residues in contact with ARG 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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132C PRO* 4.2 3.8 - - - -
161C LEU* 3.2 6.7 - - - -
162C GLU* 2.6 60.2 + - + +
203C SER* 1.3 78.2 - - - +
205C PHE* 1.3 61.9 + - - +
206C ASN* 2.9 25.1 + - + +
212C ALA 3.3 23.4 + - - +
213C GLN* 3.3 25.3 + - - +
214C HIS 4.0 9.2 - - - +
215C TRP* 3.5 50.1 - - + +
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Residues in contact with PHE 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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125A SER* 5.7 0.2 - - - -
45C VAL* 5.0 3.1 - - + -
102C LEU* 4.3 11.4 - - + -
103C TYR* 3.7 11.0 - - - -
127C GLN* 3.4 28.5 - - - -
130C VAL* 3.8 34.3 - - + -
132C PRO* 4.2 11.0 - - + +
157C LEU* 4.2 22.2 - - + -
160C CYS* 3.4 35.4 - - + -
161C LEU* 3.8 5.4 - - + +
204C ARG* 1.3 71.9 - - - +
206C ASN* 1.3 60.0 + - - +
209C CYS* 3.4 33.0 - - + -
210C GLY 3.0 14.4 - - - +
212C ALA* 3.3 15.9 - - + +
214C HIS 5.2 0.2 + - - -
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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