Contacts of the helix formed by residues 147 - 151 (chain O) in PDB entry 6R7H
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 TRP 147 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O VAL* 5.6 1.3 - - + -
87O TYR* 2.4 46.2 + + - -
90O TYR* 3.5 37.7 - + - -
91O TRP* 3.6 44.6 - + + -
94O TYR* 3.6 41.7 - + + -
143O ALA 3.5 8.1 + - - +
144O LEU* 3.4 12.0 + - - +
145O ASP 3.2 0.8 - - - -
146O MET* 1.3 77.8 - - - +
148O ARG* 1.3 61.5 + - - +
149O LYS 3.3 1.1 - - - -
150O LEU* 3.6 28.4 + - + +
151O MET* 3.4 14.1 - - + +
187O SER* 3.1 13.8 + - - -
191O VAL* 3.8 17.5 - - + -
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Residues in contact with ARG 148 (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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117O LYS* 4.6 3.4 - - - +
126O GLY 3.5 14.4 - - - +
127O TYR* 3.6 31.5 + - + -
144O LEU 3.8 7.4 - - - +
145O ASP* 3.6 8.9 + - - +
146O MET 3.5 0.6 - - - -
147O TRP* 1.3 76.1 - - - +
149O LYS* 1.3 62.7 + - - +
150O LEU 3.2 1.4 + - - -
151O MET* 3.5 18.4 + - - +
152O VAL* 3.7 17.2 + - - +
191O VAL* 3.7 25.0 + - + +
192O GLU* 3.3 23.6 + - - +
193O GLN* 3.2 49.2 + - - +
195O LYS* 3.1 38.3 - - - +
202O PHE* 3.8 16.9 - - + -
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Residues in contact with LYS 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O GLU* 4.0 19.6 + - - +
69O VAL* 4.2 11.8 - - - +
70O ARG* 3.7 32.1 + - - +
126O GLY* 3.2 17.5 + - - +
128O GLY 3.4 28.6 + - - +
129O GLY* 5.0 0.2 - - - -
130O VAL* 4.0 20.4 + - + +
134O GLU* 4.7 3.5 + - - +
145O ASP 4.3 0.4 + - - +
146O MET* 3.3 50.0 - - - +
148O ARG* 1.3 76.0 - - - +
150O LEU* 1.3 63.4 + - + +
151O MET 3.4 0.4 - - - -
152O VAL* 3.3 22.2 - - - +
153O GLU* 3.4 14.0 - - - +
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Residues in contact with LEU 150 (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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69O VAL* 3.8 25.6 - - + +
70O ARG* 3.7 15.7 - - - +
73O HIS* 3.3 55.3 + - + -
87O TYR* 5.7 7.7 - - + -
90O TYR* 4.3 10.8 - - + -
146O MET 3.8 16.4 - - - +
147O TRP* 3.8 44.2 - - + +
148O ARG 3.2 1.2 - - - -
149O LYS* 1.3 79.1 - - + +
151O MET* 1.3 63.2 + - + +
152O VAL 3.6 0.2 - - - -
153O GLU* 4.2 5.6 - - - +
155O LEU* 5.2 5.4 - - - +
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Residues in contact with MET 151 (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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87O TYR* 4.2 17.0 - - + +
147O TRP* 3.4 31.6 - - + +
148O ARG* 3.5 16.9 + - + +
150O LEU* 1.3 80.1 - - + +
152O VAL* 1.3 62.8 + - - +
153O GLU 3.2 10.4 + - - +
155O LEU* 6.3 0.2 - - - -
156O GLN* 3.4 34.6 + - + +
159O LEU* 5.8 3.8 - - + -
188O PHE* 3.6 35.2 - - + -
191O VAL* 4.6 10.5 - - + -
202O PHE* 3.9 22.2 - - + -
206O ILE* 3.7 12.3 - - + -
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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