Contacts of the strand formed by residues 156 - 161 (chain L) in PDB entry 2BDI
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 GLN 156 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L ILE* 3.4 26.7 - - + +
19L GLY 4.1 4.0 - - - +
20L GLU* 3.3 23.3 + - - +
21L ASP* 3.3 25.3 + - - +
22L CYS* 3.0 6.7 - - - -
139L SER* 2.8 30.0 - - - -
140L GLY 2.9 9.6 + - - +
144L LEU* 3.7 28.0 - - + +
152L PRO* 3.7 16.1 - - + +
154L VAL* 2.9 27.3 + - - +
155L LEU* 1.3 76.7 + - - +
157L CYS* 1.3 60.6 + - - +
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Residues in contact with CYS 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L ILE* 3.1 4.7 - - - +
19L GLY* 3.0 19.4 - - - -
20L GLU 2.9 14.7 + - - +
22L CYS* 2.1 50.3 - - + -
27L GLN* 3.9 18.6 - - - -
137L LEU* 3.8 12.8 - - + -
138L VAL 3.4 6.7 - - - -
139L SER* 3.7 11.9 - - - -
156L GLN* 1.3 76.9 - - - +
158L VAL* 1.3 71.2 + - - +
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Residues in contact with VAL 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L ILE* 3.4 20.2 - - + -
17L ILE 4.2 1.1 - - - +
18L ASN 3.5 25.8 - - - +
19L GLY* 3.8 3.1 - - - -
137L LEU* 3.2 7.2 - - - +
138L VAL* 3.0 49.4 + - + +
157L CYS* 1.3 80.3 - - - +
159L ASN* 1.3 73.6 + - - +
160L VAL* 4.3 9.0 - - + -
188L LYS* 3.7 28.0 - - + +
189L ASP 4.5 9.4 - - - +
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Residues in contact with ASN 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L SER* 3.6 16.0 + - - +
136L CYS* 3.0 22.5 + - - +
137L LEU* 3.9 15.4 - - - +
158L VAL* 1.3 82.2 - - - +
160L VAL* 1.3 68.8 + - - +
186L ASP* 5.1 1.6 - - - +
188L LYS* 3.7 28.1 + - - +
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Residues in contact with VAL 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L SER* 4.5 0.9 - - - -
136L CYS* 3.0 27.0 + - - +
138L VAL* 3.8 21.1 - - + -
158L VAL* 4.3 10.8 - - + -
159L ASN* 1.3 81.8 - - - +
161L SER* 1.3 63.1 + - - +
183L ALA* 3.9 20.3 - - + +
184L GLY* 3.7 16.2 - - - -
188L LYS* 3.6 29.8 - - + +
189L ASP* 4.4 5.4 - - - -
199L LEU* 4.0 10.3 - - + -
228L TYR* 4.4 4.5 - - - +
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Residues in contact with SER 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I ASN* 5.9 2.9 - - - -
133L GLY* 3.5 16.5 + - - -
134L ASN 3.0 11.4 - - - -
135L SER* 3.7 15.6 + - - -
160L VAL* 1.3 77.8 - - - +
162L VAL* 1.3 70.9 + - - +
163L VAL* 3.3 2.8 + - - +
183L ALA* 3.1 2.1 - - - -
184L GLY* 2.7 31.3 + - - +
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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