Contacts of the strand formed by residues 135 - 140 (chain J) 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 SER 135 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133J GLY 3.5 3.0 + - - -
134J ASN* 1.3 85.6 + - - +
136J CYS* 1.3 70.1 + - - +
159J ASN* 3.6 16.1 + - - +
160J VAL 4.2 1.2 + - - -
161J SER* 3.7 17.1 + - - -
201J CYS* 5.0 0.7 - - - +
202J ASN* 5.0 5.7 + - - -
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Residues in contact with CYS 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J ASN* 3.8 15.9 - - - -
135J SER* 1.3 79.5 + - - +
137J LEU* 1.4 56.0 - - - +
159J ASN* 2.7 24.9 + - - +
160J VAL* 2.9 28.7 + - + +
162J VAL* 3.9 12.3 - - - -
199J LEU* 4.4 10.5 - - + -
200J ILE 2.8 19.7 - - - +
201J CYS* 2.1 41.5 - - + +
202J ASN 5.7 0.2 - - - +
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J GLN* 3.6 35.2 - - - +
136J CYS* 1.4 77.1 - - - +
138J VAL* 1.3 68.1 + - - +
139J SER* 5.2 1.3 - - - +
157J CYS* 3.9 16.6 - - + -
158J VAL 3.2 31.6 - - - +
159J ASN* 3.9 16.8 - - - +
198J PRO 3.8 0.3 - - - +
199J LEU* 3.2 5.7 - - - -
200J ILE* 2.7 45.6 + - + +
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Residues in contact with VAL 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J ILE* 3.8 18.4 - - + +
137J LEU* 1.3 78.7 - - - +
139J SER* 1.3 65.5 + - - +
157J CYS* 3.6 0.9 - - - -
158J VAL* 2.9 46.2 + - + +
160J VAL* 3.8 16.4 - - + -
190J SER* 4.0 16.6 - - - +
198J PRO 3.2 15.9 - - - +
199J LEU* 3.5 18.4 - - + -
200J ILE* 6.1 0.2 - - - -
213J VAL* 4.3 13.7 - - + -
228J TYR* 4.1 6.7 - - + +
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Residues in contact with SER 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J ILE* 3.7 7.8 - - - +
22J CYS* 4.1 1.6 - - - -
27J GLN* 4.1 10.8 + - - +
30J GLN* 2.8 35.8 + - - +
137J LEU* 5.2 1.8 - - - +
138J VAL* 1.3 78.9 - - - +
140J GLY* 1.3 58.2 + - - +
155J LEU* 4.1 7.9 - - - -
156J GLN 2.9 18.6 - - - -
157J CYS* 3.9 15.3 - - - -
194J ASP* 5.2 1.9 - - - +
197J GLY* 4.2 5.7 - - - -
198J PRO* 3.5 21.5 + - - +
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Residues in contact with GLY 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J ILE* 3.5 5.4 - - - +
30J GLN* 3.7 5.2 - - - -
43J SER* 4.5 5.6 - - - -
139J SER* 1.3 75.0 - - - +
141J TRP* 1.3 59.3 + - - -
142J GLY 3.3 4.9 - - - -
155J LEU* 3.2 15.3 - - - +
156J GLN* 3.0 35.3 + - - +
194J ASP* 3.3 13.0 - - - -
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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