Contacts of the strand formed by residues 162 - 169 (chain C) in PDB entry 2B5I
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 GLU 162 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ARG* 2.7 48.5 + - - +
161C LEU* 1.3 74.0 - - - +
163C HIS* 1.3 73.5 + - - +
179C SER* 5.4 0.4 - - - -
180C VAL 3.4 9.2 - - - +
181C ASP* 4.5 1.6 - - - -
203C SER* 3.8 0.3 - - - -
204C ARG* 2.8 75.2 + - + +
206C ASN* 2.9 32.4 + - - +
207C PRO* 4.1 0.7 - - + +
215C TRP* 4.3 7.9 - - + -
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Residues in contact with HIS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG* 4.7 0.3 + - - -
152C TRP* 3.4 31.8 + + + -
154C ASN* 3.3 29.2 - - - -
158C ASN* 5.0 1.8 + - - -
161C LEU* 3.8 26.3 + - + +
162C GLU* 1.3 76.2 + - - +
164C LEU* 1.3 60.9 + - - +
165C VAL 4.1 0.2 - - - -
179C SER* 3.5 6.9 + - - -
180C VAL* 2.7 45.8 + - + +
181C ASP 3.2 24.4 + - - -
182C TYR* 4.7 3.0 - - - -
184C HIS* 3.7 12.4 + - + +
201C VAL* 4.1 2.7 - - + +
202C ARG 3.3 7.9 - - - +
203C SER* 2.9 21.3 + - - -
215C TRP* 3.8 7.8 - - - -
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Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C HIS* 1.3 75.3 - - - +
165C VAL* 1.3 68.3 + - - +
166C GLN* 4.5 6.3 - - + +
177C GLU* 4.0 35.7 - - + +
178C GLN 3.7 16.8 - - - +
179C SER* 4.2 9.4 - - - +
201C VAL* 3.3 6.0 - - - +
202C ARG* 2.9 65.9 + - + +
215C TRP* 3.6 25.1 - - + -
218C TRP* 3.7 14.3 - - + -
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LEU* 3.9 14.4 - - + -
152C TRP* 3.5 34.3 - - + -
164C LEU* 1.3 74.8 - - - +
166C GLN* 1.3 71.7 + - - +
167C TYR* 4.8 3.5 - - + -
176C THR 3.6 0.5 - - - +
177C GLU* 3.1 6.1 - - - +
178C GLN* 2.8 41.2 + - + +
180C VAL* 3.9 17.9 - - + -
186C PHE* 3.9 36.6 - - + -
199C PHE* 5.0 1.8 - - + -
200C ARG 3.6 5.6 - - - +
201C VAL* 4.3 3.6 - - + -
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Residues in contact with GLN 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LEU* 4.0 5.5 + - + +
165C VAL* 1.3 79.4 - - - +
167C TYR* 1.3 60.6 + - - +
175C TRP* 3.4 38.4 - - + +
176C THR 3.1 2.2 - - - +
177C GLU* 4.0 24.9 + - + +
199C PHE* 3.4 2.9 - - - +
200C ARG* 2.8 76.4 + - + +
202C ARG* 5.6 1.2 - - - +
218C TRP* 3.4 24.1 - - + -
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Residues in contact with TYR 167 (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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166B TRP* 3.6 17.3 - + - -
168B CYS* 5.6 1.0 - - - +
165C VAL* 4.8 3.1 - - + -
166C GLN* 1.3 74.7 - - - +
168C ARG* 1.3 66.0 + - - +
169C THR* 5.6 0.7 - - + -
172C ASP* 5.3 3.8 - - - -
175C TRP* 3.6 4.7 - - - -
176C THR* 2.6 82.0 + - + +
177C GLU 6.1 0.2 - - - -
178C GLN* 5.8 2.0 - - + -
186C PHE* 3.9 33.7 - + - -
188C LEU* 3.5 25.4 - - + +
197C TYR* 4.2 21.3 - + + -
198C THR 3.1 14.1 - - - +
199C PHE* 3.4 23.6 - + + -
1E NAG 4.2 6.1 - - + +
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Residues in contact with ARG 168 (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* 1.3 81.4 - - - +
169C THR* 1.3 73.0 + - - +
170C ASP* 5.5 5.3 + - - +
172C ASP* 3.3 19.9 + - + +
174C SER* 3.3 27.0 - - - +
175C TRP* 3.5 48.9 - - + +
197C TYR* 3.4 2.6 - - - +
198C THR* 2.8 45.0 + - - +
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Residues in contact with THR 169 (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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170B GLU* 5.9 2.0 - - - +
167C TYR* 5.4 2.2 - - + -
168C ARG* 1.3 82.9 + - - +
170C ASP* 1.3 56.2 + - - +
171C TRP* 2.7 30.0 + - - +
172C ASP* 2.6 50.6 + - - +
195C LYS* 3.9 22.9 + - + +
196C ARG 3.0 9.9 - - - -
197C TYR* 3.5 38.8 - - + +
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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