Contacts of the helix formed by residues 138 - 146 (chain H) in PDB entry 7CR3
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 ASN 138 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G ASN* 4.1 10.0 + - - +
150G CYS* 3.1 21.4 - - - -
98H ASN 5.4 0.2 - - - +
99H GLY* 3.3 14.7 - - - +
100H TYR* 3.8 21.7 + - + -
136H GLN 3.7 3.8 + - - +
137H VAL* 1.3 72.8 - - - +
139H TYR* 1.3 65.5 + - - +
140H GLU* 2.9 43.6 + - - +
141H GLU* 2.8 45.7 + - - +
142H PHE 3.7 0.2 + - - -
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Residues in contact with TYR 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H ARG* 3.5 46.9 + - + +
90H PHE* 3.5 49.6 - + + -
91H ARG* 5.2 7.2 - - - +
94H ASP* 3.7 14.4 + - - -
99H GLY* 3.4 35.0 - - - +
101H ILE* 5.3 5.4 - - + -
137H VAL* 3.3 15.3 + - + +
138H ASN* 1.3 72.0 - - - +
140H GLU* 1.3 74.1 + - - +
142H PHE* 3.1 7.7 + - - +
143H VAL* 3.0 30.5 + - - +
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Residues in contact with GLU 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G ASN* 4.8 1.0 - - - +
82G TYR* 3.5 21.3 + - - -
83G ASN* 5.1 4.2 + - - -
150G CYS* 3.3 16.8 - - - +
151G CYS* 5.9 0.2 - - - -
87H ARG* 4.5 14.0 - - - +
98H ASN 5.8 0.2 - - - +
99H GLY* 5.8 0.6 - - - -
100H TYR* 5.5 0.2 + - - -
138H ASN* 2.9 36.6 + - - +
139H TYR* 1.3 96.2 + - + +
141H GLU* 1.3 60.2 + - - +
143H VAL* 3.6 9.2 - - - -
144H GLN* 2.9 50.6 + - - +
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Residues in contact with GLU 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G CYS* 4.3 18.1 - - - +
152G CYS* 4.5 5.7 - - + +
129H ALA 2.9 23.1 - - - +
130H ASP* 3.8 5.7 - - - +
131H ILE* 3.1 32.7 + - + +
132H ASP* 4.6 4.3 - - - +
138H ASN* 2.8 40.9 + - + +
140H GLU* 1.3 80.9 - - - +
142H PHE* 1.3 58.2 + - - +
144H GLN* 3.8 3.6 - - - -
145H MET* 3.0 29.8 + - - +
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Residues in contact with PHE 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340G ILE* 5.5 6.7 - - + -
344G TRP* 3.9 19.3 - + - -
86H ILE* 6.0 4.3 - - + -
90H PHE* 4.2 24.7 - + - -
125H MET* 4.7 5.2 - - + -
128H GLU* 3.3 31.6 - - + -
129H ALA* 3.4 32.1 - - + +
137H VAL* 5.1 0.2 - - + -
139H TYR* 3.1 13.8 + - - +
141H GLU* 1.3 84.2 - - - +
143H VAL* 1.3 59.5 - - + +
145H MET* 3.3 7.7 + - + +
146H MET* 3.0 69.8 + - + +
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Residues in contact with VAL 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H GLU* 3.2 23.6 - - - +
86H ILE* 3.5 34.1 - - + -
87H ARG* 3.6 16.2 - - + -
90H PHE* 3.6 26.9 - - + -
139H TYR 3.0 15.9 + - - +
140H GLU* 3.3 17.7 - - - +
142H PHE* 1.3 78.8 - - + +
144H GLN* 1.3 61.6 + - + +
147H THR* 3.0 35.7 + - - +
148H ALA 3.4 1.7 + - - -
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Residues in contact with GLN 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G TYR* 5.5 3.4 + - - -
151G CYS* 2.6 47.2 - - - +
152G CYS* 3.3 28.4 + - + +
153G ARG* 4.2 20.1 + - + +
83H GLU* 3.5 21.1 - - - +
87H ARG* 4.5 10.0 - - - +
140H GLU* 2.9 38.0 + - - +
141H GLU 4.3 0.2 + - - -
143H VAL* 1.3 74.6 - - + +
145H MET* 1.3 60.2 + - - +
148H ALA* 3.9 16.1 - - - +
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Residues in contact with MET 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G CYS* 3.9 15.9 - - - -
347G TYR* 5.6 0.4 - - - -
353G ARG* 4.8 5.8 - - - -
128H GLU* 3.2 46.7 - - - +
131H ILE* 3.8 16.6 - - + -
141H GLU 3.0 18.2 + - - +
142H PHE* 3.6 6.1 - - + +
143H VAL 3.2 0.6 - - - -
144H GLN* 1.3 80.1 - - - +
146H MET* 1.3 86.5 + - + +
148H ALA 4.6 5.8 + - - +
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Residues in contact with MET 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343G ALA 5.4 0.9 - - - +
344G TRP* 4.5 2.7 - - + -
347G TYR* 3.4 61.9 - - + -
76H LYS* 6.0 0.3 + - - -
77H MET* 3.8 27.3 - - + +
128H GLU* 3.9 4.7 - - - -
142H PHE* 3.0 52.5 + - + +
145H MET* 1.3 92.2 - - - +
147H THR* 1.3 68.5 + - - +
148H ALA 2.9 13.2 - - - +
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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