Contacts of the strand formed by residues 135 - 140 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133K GLY 3.4 2.3 + - - -
134K ASN* 1.3 85.7 + - - +
136K CYS* 1.4 62.3 + - - +
159K ASN* 3.6 24.4 + - - +
160K VAL 3.8 1.7 + - - -
161K SER* 3.7 16.8 + - - -
201K CYS* 4.9 2.8 - - - -
202K ASN* 4.9 5.0 + - - -
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Residues in contact with CYS 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K ASN* 3.9 12.6 - - - -
135K SER* 1.4 77.7 - - - +
137K LEU* 1.3 59.6 + - - +
159K ASN* 3.2 12.9 + - - +
160K VAL* 2.9 31.8 + - + +
162K VAL* 3.9 11.7 - - - -
199K LEU* 4.2 13.0 - - + -
200K ILE 2.7 21.1 - - - +
201K CYS* 2.1 42.6 - - - +
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Residues in contact with LEU 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TYR* 6.1 2.0 - - - +
27K GLN* 3.5 36.8 - - - +
136K CYS* 1.3 78.2 - - - +
138K VAL* 1.4 67.0 + - - +
139K SER* 5.1 1.3 - - - +
157K CYS* 3.7 24.0 - - + -
158K VAL 3.3 22.0 - - - +
159K ASN* 3.9 18.8 - - - +
198K PRO 3.8 0.3 - - - +
199K LEU* 3.3 4.6 - - - +
200K ILE* 2.7 43.9 + - + +
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Residues in contact with VAL 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ILE* 3.9 18.2 - - + +
137K LEU* 1.4 77.4 - - - +
139K SER* 1.3 64.6 + - - +
157K CYS* 3.3 3.3 - - - -
158K VAL* 3.0 47.2 + - + +
160K VAL* 3.8 14.4 - - + -
190K SER* 4.0 16.2 - - - +
198K PRO 3.2 15.3 - - - +
199K LEU* 3.5 19.1 - - + -
200K ILE* 6.1 0.2 - - - -
213K VAL* 4.2 15.3 - - + -
228K TYR* 4.1 6.7 - - + +
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Residues in contact with SER 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ILE* 3.7 8.9 - - - +
22K CYS* 4.0 4.5 - - - -
27K GLN* 4.1 11.6 + - - +
30K GLN* 2.8 35.5 + - - +
137K LEU* 5.1 1.6 - - - +
138K VAL* 1.3 78.5 - - - +
140K GLY* 1.3 57.3 + - - +
155K LEU* 4.1 5.2 - - - -
156K GLN 2.9 18.8 - - - -
157K CYS* 3.8 15.0 - - - -
194K ASP* 5.2 2.1 - - - +
197K GLY* 4.2 5.7 - - - -
198K PRO* 3.6 19.4 + - - +
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Residues in contact with GLY 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ILE* 3.5 5.1 - - - +
30K GLN* 3.7 5.6 - - - -
43K SER* 4.5 5.4 - - - -
139K SER* 1.3 74.4 - - - +
141K TRP* 1.3 59.6 + - - -
142K GLY 3.3 5.1 + - - -
155K LEU* 3.2 17.4 - - - +
156K GLN* 3.0 34.1 + - - +
194K 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