Contacts of the strand formed by residues 136 - 142 (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 GLU 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C TRP* 5.5 0.2 - - - +
134C ALA 4.4 6.0 - - - +
135C PRO* 1.3 76.2 - - + +
137C ASN* 1.3 88.1 + - - +
138C LEU* 3.3 8.9 + - - +
153C ASN* 3.1 35.8 + - - +
154C ASN* 5.8 0.2 - - - -
155C ARG* 2.9 45.8 + - - +
220C HIS* 6.4 1.8 - - + -
941C NAG 3.8 19.5 - - - +
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Residues in contact with ASN 137 (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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136C GLU* 1.3 92.5 - - - +
138C LEU* 1.3 67.7 + - - +
139C THR* 3.5 14.7 + - + +
152C TRP* 4.1 4.7 - - - -
153C ASN* 3.2 14.9 - - - +
941C NAG 1.5 63.8 + - - +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C PRO* 4.0 2.2 - - + +
136C GLU* 3.7 25.6 - - - +
137C ASN* 1.3 77.6 - - - +
139C THR* 1.3 60.2 + - - +
150C LEU* 4.4 11.0 - - + -
151C ASN 3.3 8.1 - - - +
152C TRP* 3.9 17.0 - - + -
199C PHE 4.4 6.1 - - - +
200C ARG* 4.4 5.8 - - - -
201C VAL* 4.6 7.6 - - + +
219C SER* 3.2 33.9 - - - +
220C HIS 3.8 12.8 - - - +
221C PRO 5.7 0.4 - - - +
222C ILE* 3.2 37.7 - - + +
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Residues in contact with THR 139 (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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137C ASN* 3.5 16.2 - - + +
138C LEU* 1.3 74.1 - - - +
140C LEU* 1.3 63.8 + - - +
141C HIS* 4.4 8.3 - - - -
150C LEU* 3.1 23.9 - - - +
151C ASN* 3.1 39.7 + - + +
222C ILE* 3.8 3.6 - - - -
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Residues in contact with LEU 140 (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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139C THR* 1.3 81.8 - - - +
141C HIS* 1.3 61.7 + - - +
148C LEU* 3.7 34.5 - - + +
149C GLU 3.8 9.0 - - - +
150C LEU* 4.1 15.3 - - + +
199C PHE* 3.8 29.6 - - + -
222C ILE* 3.8 22.5 - - + +
223C HIS 3.5 23.6 - - - +
224C TRP* 3.3 29.6 - - + -
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Residues in contact with HIS 141 (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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139C THR* 4.4 9.6 - - - -
140C LEU* 1.3 76.5 - - - +
142C LYS* 1.3 70.1 + - - +
143C LEU* 3.4 28.9 - - + -
148C LEU* 3.3 8.6 - - - +
149C GLU* 3.1 43.8 + - + -
151C ASN* 3.3 25.2 + - - -
224C TRP* 4.5 2.5 - - - -
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Residues in contact with LYS 142 (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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141C HIS* 1.3 81.9 + - - +
143C LEU* 1.3 61.8 + - - +
144C SER 3.1 21.8 - - - +
145C GLU 3.5 9.7 + - - +
146C SER* 3.2 32.9 + - - +
147C GLN 3.6 8.3 - - - +
148C LEU* 4.2 5.6 - - + +
191C VAL* 3.8 21.4 - - - +
224C TRP* 3.9 35.9 - - + +
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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