Contacts of the strand formed by residues 133 - 138 (chain B) in PDB entry 6BM0
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 ARG 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B TRP* 4.1 4.4 - - - -
128B THR* 2.9 48.3 + - - +
131B GLY 3.4 2.0 + - - -
132B ARG* 1.3 116.6 - - + +
134B LEU* 1.3 62.3 + - - +
135B VAL* 5.5 0.4 - - + +
145B LEU* 3.7 27.4 - - + +
146B TRP 3.2 13.5 - - - +
148B GLY* 4.2 2.9 - - - +
154B GLU* 3.0 38.0 + - - +
155B THR* 6.0 0.6 - - - +
190B SER 5.6 5.0 + - - -
191B ASN* 6.4 0.2 - - - +
192B MET* 5.9 2.2 - - + +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL* 3.7 16.4 - - + -
126B ARG 3.3 22.7 - - - +
127B TRP* 3.5 57.0 - - + +
133B ARG* 1.3 71.7 - - - +
135B VAL* 1.3 60.6 + - - +
144B THR 3.5 2.4 - - - +
145B LEU* 3.2 2.9 - - - -
146B TRP* 2.5 53.1 + - + +
147B ASN 4.8 2.2 - - - +
391B CYS* 3.9 10.5 - - + -
401B PHE* 3.6 36.6 - - + -
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 3.5 3.3 - - - +
126B ARG 3.2 32.4 + - - +
128B THR* 5.2 2.5 - - - +
133B ARG* 3.9 3.2 + - + +
134B LEU* 1.3 73.0 - - - +
136B THR* 1.3 67.6 + - - +
143B PHE* 3.8 36.1 - - + -
144B THR 4.0 2.5 - - - -
145B LEU* 3.8 17.5 - - + +
167B MET* 3.7 21.8 - - + -
169B TRP* 4.2 17.0 - - + +
176B MET* 4.3 6.7 - - + -
192B MET* 4.1 18.2 - - + -
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ASN* 5.4 1.1 - - - +
122B VAL* 3.7 29.8 - - + -
124B VAL 3.9 2.9 - - - -
125B VAL* 3.7 24.5 - - + +
134B LEU 4.4 0.3 + - - -
135B VAL* 1.3 79.4 + - - +
137B GLY* 1.3 61.1 + - - +
138B ALA* 4.9 0.8 - - + +
142B GLU 3.0 17.7 - - - +
143B PHE* 3.4 4.9 - - - -
144B THR* 3.3 32.8 + - - +
146B TRP* 3.2 24.6 - - - +
399B SER* 5.3 6.4 + - - -
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B VAL* 3.4 6.7 - - - +
123B PHE 2.9 25.1 + - - -
124B VAL* 2.7 23.3 + - - +
135B VAL 4.3 0.2 - - - -
136B THR* 1.3 71.8 - - - +
138B ALA* 1.3 62.1 + - - -
142B GLU 3.9 3.4 - - - -
143B PHE* 4.2 12.6 - - - -
164B VAL* 4.2 17.7 - - - -
167B MET* 4.4 3.6 - - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ASN* 4.8 9.6 - - - +
120B CYS* 4.3 14.8 - - + +
121B PRO 3.6 8.1 - - - +
122B VAL* 3.8 18.4 - - + +
123B PHE* 4.2 4.5 - - - -
136B THR* 4.9 1.3 - - + +
137B GLY* 1.3 73.5 - - - -
139B SER* 1.3 66.7 + - - +
140B SER* 3.3 7.9 - - - +
141B GLY 3.4 6.7 + - - -
142B GLU* 3.5 19.7 + - + +
144B THR* 5.9 0.7 - - + -
164B VAL* 3.2 21.6 + - - +
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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