Contacts of the strand formed by residues 135 - 140 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133O GLY 3.4 2.3 + - - -
134O ASN* 1.3 86.4 + - - +
136O CYS* 1.4 61.8 + - - +
159O ASN* 3.6 23.1 + - - +
160O VAL 3.8 1.4 + - - -
161O SER* 3.7 17.3 + - - -
201O CYS* 4.9 2.6 - - - -
202O ASN* 5.0 4.9 + - - -
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Residues in contact with CYS 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O ASN* 3.8 12.3 - - - -
135O SER* 1.4 77.8 - - - +
137O LEU* 1.3 63.8 + - - +
159O ASN* 3.2 12.6 + - - +
160O VAL* 2.9 32.9 + - + +
162O VAL* 3.9 10.8 - - - -
199O LEU* 4.1 16.8 - - + -
200O ILE 2.9 15.0 - - - +
201O CYS* 2.1 42.0 - - - +
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Residues in contact with LEU 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O GLN* 3.5 36.6 - - - +
136O CYS* 1.3 78.3 - - - +
138O VAL* 1.3 68.7 + - - +
139O SER* 5.1 1.6 - - - +
157O CYS* 4.0 16.2 - - + -
158O VAL 3.3 31.0 - - - +
159O ASN* 3.9 17.5 - - - +
198O PRO 3.7 0.3 - - - +
199O LEU* 3.2 4.8 - - - -
200O ILE* 2.8 45.3 + - + +
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Residues in contact with VAL 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O ILE* 3.9 18.0 - - + +
137O LEU* 1.3 77.9 - - - +
139O SER* 1.3 64.4 + - - +
157O CYS* 3.4 2.1 - - - -
158O VAL* 2.9 47.8 + - + +
160O VAL* 3.8 14.6 - - + -
190O SER* 4.0 16.4 - - - +
198O PRO 3.1 15.5 - - - +
199O LEU* 3.5 20.2 - - + -
213O VAL* 4.2 14.6 - - + -
228O TYR* 4.1 6.5 - - + +
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Residues in contact with SER 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O ILE* 3.7 7.9 - - - +
22O CYS* 4.3 9.4 - - - -
27O GLN* 4.1 12.4 + - - +
30O GLN* 2.9 35.2 + - - +
137O LEU* 5.1 1.5 - - - +
138O VAL* 1.3 79.6 - - - +
140O GLY* 1.3 58.2 + - - +
155O LEU* 4.1 10.1 - - - -
156O GLN 2.8 18.4 - - - -
157O CYS* 4.3 3.6 - - - -
194O ASP* 5.2 1.6 - - - +
197O GLY* 4.2 6.4 - - - -
198O PRO* 3.5 20.6 + - - +
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Residues in contact with GLY 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O ILE* 3.5 5.7 - - - +
30O GLN* 3.7 5.6 - - - -
43O SER* 4.5 5.4 - - - -
139O SER* 1.3 75.1 - - - +
141O TRP* 1.3 59.1 + - - -
142O GLY 3.3 5.4 - - - -
155O LEU* 3.2 16.2 - - - +
156O GLN* 3.0 34.3 + - - +
194O ASP* 3.3 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