Contacts of the strand formed by residues 147 - 152 (chain B) in PDB entry 6CNC
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 VAL 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B TYR* 3.3 3.9 - - - -
131B VAL* 2.8 51.3 + - + +
133B ILE* 4.8 9.9 - - + -
145B LYS* 4.1 30.5 - - + -
146B ASP* 1.3 85.2 + - - +
148B GLU* 1.3 70.8 + - - +
419B LEU* 5.2 6.3 - - + -
422B ILE* 3.5 34.1 - - + -
423B ASN* 4.8 5.6 - - - +
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Residues in contact with GLU 148 (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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103B LYS* 5.7 1.6 - - - +
128B PRO* 4.5 9.9 - - + -
129B ILE 3.3 8.5 - - - +
130B TYR* 3.2 35.4 + - + -
146B ASP 4.7 3.2 - - - +
147B VAL* 1.3 87.3 - - - +
149B ILE* 1.3 61.7 + - - +
150B GLY* 4.3 7.0 - - - +
422B ILE* 3.5 9.0 - - - +
423B ASN* 3.6 17.4 + - - +
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Residues in contact with ILE 149 (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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95B TYR* 5.9 4.0 - - + -
129B ILE* 3.5 36.5 + - + -
131B VAL* 3.6 33.9 - - + -
133B ILE* 5.7 1.3 - - + -
147B VAL 3.7 1.4 + - - -
148B GLU* 1.3 75.5 - - - +
150B GLY* 1.3 57.3 + - - +
388B PHE* 5.2 6.5 - - + -
392B PHE* 5.6 9.0 - - + -
395B PHE* 4.7 22.7 - - + -
422B ILE* 4.6 13.5 - - + -
426B SER* 3.2 21.0 - - - -
429B ILE* 3.2 44.5 - - + +
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Residues in contact with GLY 150 (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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128B PRO* 3.5 4.0 - - - +
129B ILE* 2.6 38.8 + - - +
148B GLU* 3.4 6.4 - - - +
149B ILE* 1.3 79.3 - - - +
151B ARG* 1.3 58.4 + - - +
426B SER* 5.0 3.6 - - - -
427B ASN* 5.2 1.3 - - - -
429B ILE* 4.3 3.1 - - - -
430B THR* 3.2 11.2 - - - -
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Residues in contact with ARG 151 (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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124B THR* 5.8 5.9 - - - +
126B SER* 3.0 28.3 + - - +
127B ALA 3.7 2.7 - - - -
128B PRO* 3.6 25.6 - - + -
129B ILE* 4.3 1.3 - - - +
150B GLY* 1.3 76.8 - - - -
152B MET* 1.3 60.6 + - - +
153B PRO* 3.9 4.9 - - - +
429B ILE* 5.3 0.2 - - - +
430B THR* 2.4 50.3 + - + +
433B LEU* 5.0 1.4 - - - +
434B ASN* 4.7 1.2 + - - -
890B ASP* 5.4 6.3 + - - +
95R HIS* 4.6 20.6 + - - -
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Residues in contact with MET 152 (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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65B PHE* 4.0 21.8 - - + -
68B PHE* 3.5 32.1 - - + -
69B VAL* 5.1 2.5 - - + -
73B LEU* 5.9 1.6 - - + -
100B VAL* 4.7 8.5 - - + -
126B SER* 2.8 14.0 + - - -
127B ALA 2.9 22.0 + - - +
129B ILE* 3.4 28.9 - - + +
151B ARG* 1.3 72.4 - - - +
153B PRO* 1.3 80.3 - - + +
154B ILE* 3.2 13.3 + - + +
384B ILE* 3.7 22.0 - - + -
388B PHE* 4.9 10.5 - - - -
433B LEU* 3.6 15.9 - - + -
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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