Contacts of the strand formed by residues 135 - 140 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D GLY 3.4 2.1 + - - -
134D ASN* 1.3 85.3 + - - +
136D CYS* 1.3 63.9 + - - +
159D ASN* 3.6 23.3 + - - +
160D VAL 3.8 1.3 + - - -
161D SER* 3.6 17.6 + - - -
201D CYS* 5.0 1.6 - - - -
202D ASN* 5.0 5.2 + - - -
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Residues in contact with CYS 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ASN* 4.0 4.9 - - - -
135D SER* 1.3 79.2 + - - +
137D LEU* 1.3 59.8 + - - +
159D ASN* 3.2 13.1 + - - +
160D VAL* 2.9 32.2 + - - +
162D VAL* 3.9 21.1 - - - -
199D LEU* 4.2 14.1 - - + -
200D ILE 2.8 18.2 - - - +
201D CYS* 2.1 43.7 - - - +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLN* 3.5 36.3 - - - +
136D CYS* 1.3 79.5 - - - +
138D VAL* 1.3 68.5 + - - +
139D SER* 5.2 1.6 - - - +
157D CYS* 4.0 16.8 - - + -
158D VAL 3.3 31.0 - - - +
159D ASN* 3.9 18.2 - - - +
198D PRO 3.8 0.3 - - - +
199D LEU* 3.2 4.2 - - - -
200D ILE* 2.8 45.8 + - + +
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.9 18.5 - - + +
137D LEU* 1.3 78.3 - - - +
139D SER* 1.3 66.2 + - - +
157D CYS* 3.6 0.7 - - - -
158D VAL* 2.9 46.7 + - + +
160D VAL* 3.8 16.2 - - + -
190D SER* 4.0 16.6 - - - +
198D PRO* 3.2 16.2 - - - +
199D LEU* 3.5 20.2 - - + -
213D VAL* 4.2 13.7 - - + -
228D TYR* 4.1 7.0 - - + +
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Residues in contact with SER 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.7 8.4 - - - +
22D CYS* 4.1 14.4 - - - -
27D GLN* 4.1 13.6 + - - +
30D GLN* 2.8 35.9 + - - +
137D LEU* 5.2 2.2 - - - +
138D VAL* 1.3 79.0 - - - +
140D GLY* 1.3 57.4 + - - +
155D LEU* 4.1 4.5 - - - -
156D GLN 2.9 18.2 - - - -
157D CYS* 4.5 1.8 - - - -
194D ASP* 5.2 1.6 - - - +
197D GLY* 4.2 5.9 - - - -
198D PRO* 3.5 20.3 + - - +
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Residues in contact with GLY 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.5 5.5 - - - +
30D GLN* 3.7 5.4 - - - -
43D SER* 4.5 5.2 - - - -
139D SER* 1.3 75.1 - - - +
141D TRP* 1.3 59.6 + - - -
142D GLY 3.3 4.9 - - - -
155D LEU* 3.2 16.2 - - - +
156D GLN* 3.0 34.6 + - - +
194D ASP* 3.4 13.5 - - - -
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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