Contacts of the helix formed by residues 102 - 111 (chain F) 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 SER 102 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101F ILE* 1.3 75.4 - - - +
103F ALA* 1.3 63.7 + - - +
104F ALA* 3.7 6.9 + - - +
105F GLU* 3.0 24.6 + - - +
106F LEU* 3.0 21.7 + - - +
135F GLY 3.7 4.7 - - - -
136F GLN* 5.0 1.8 - - - +
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F SER* 1.3 74.2 - - - +
104F ALA* 1.3 56.5 + - - +
106F LEU* 3.2 14.3 + - - +
107F ARG* 3.0 55.7 + - - +
126F ILE* 4.0 14.3 - - + +
135F GLY* 2.9 32.9 + - - +
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F SER* 3.2 7.0 + - - +
103F ALA* 1.3 75.5 - - - +
105F GLU* 1.3 57.8 + - - +
107F ARG* 3.2 23.8 + - - +
108F HIS* 2.9 28.4 + - - +
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Residues in contact with GLU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F LYS* 3.9 18.3 + - + +
101F ILE* 3.7 19.7 - - + -
102F SER* 3.0 23.7 + - - +
104F ALA* 1.3 73.3 - - - +
106F LEU* 1.3 65.5 + - - +
108F HIS* 4.0 16.1 - - - +
109F VAL* 2.9 46.7 + - + +
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F PHE* 5.8 7.6 - - + -
101F ILE* 3.6 32.3 - - + -
102F SER 3.0 10.6 + - - +
103F ALA* 3.2 18.4 + - - +
105F GLU* 1.3 74.8 - - - +
107F ARG* 1.3 57.1 + - - +
109F VAL* 5.1 1.8 - - - -
110F MET* 2.8 42.8 + - + +
122F VAL* 4.1 6.1 - - + -
125F MET 6.1 0.2 - - - -
126F ILE* 3.8 21.3 - - + -
129F ALA* 6.2 1.1 - - + -
137F VAL* 3.6 31.6 - - + -
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Residues in contact with ARG 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ALA* 3.0 31.5 + - - +
104F ALA* 3.2 34.1 - - - +
105F GLU 3.3 0.2 - - - -
106F LEU* 1.3 74.7 - - - +
108F HIS* 1.3 57.9 + - - +
111F THR* 2.2 39.0 + - + +
119F ASP* 6.4 0.7 - - + -
122F VAL* 3.7 33.7 - - + -
123F ASP* 3.0 24.4 + - - +
126F ILE* 3.3 14.2 - - + +
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Residues in contact with HIS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ALA 2.9 20.1 + - - +
105F GLU* 3.8 19.1 - - - +
106F LEU 3.4 0.2 - - - -
107F ARG* 1.3 74.3 - - - +
109F VAL* 1.3 81.0 + - + +
111F THR* 3.7 2.5 + - - -
112F ASN* 3.2 45.0 + - + +
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Residues in contact with VAL 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ALA* 4.6 4.0 - - + -
93F PHE* 3.5 34.5 - - + -
95F LYS* 4.5 9.0 - - - +
105F GLU* 2.9 43.4 + - + +
106F LEU* 4.3 2.0 - - - +
108F HIS* 1.3 85.0 - - + +
110F MET* 1.3 66.4 + - + +
112F ASN* 3.1 1.4 + - - -
113F LEU* 2.9 44.8 + - + +
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Residues in contact with MET 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ALA* 4.1 8.1 - - - +
340A ILE* 3.6 36.6 - - + -
341A GLN* 2.9 62.4 + - + +
90F PHE* 6.1 0.9 - - + -
106F LEU* 2.8 31.6 + - + +
109F VAL* 1.3 76.8 - - + +
111F THR* 1.3 58.8 + - + +
112F ASN 3.5 0.2 + - - -
113F LEU* 5.2 0.2 - - - -
116F LYS* 3.5 5.2 - - - -
117F LEU* 4.0 5.1 + - + -
122F VAL* 4.1 12.6 - - + -
125F MET* 3.7 33.0 - - + +
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Residues in contact with THR 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ARG* 2.2 33.6 + - + +
108F HIS* 3.7 4.2 + - - -
110F MET* 1.3 76.8 - - + +
112F ASN* 1.3 59.0 + - - +
116F LYS* 3.3 22.8 - - - +
117F LEU* 3.3 24.4 - - - +
118F THR 3.5 18.6 - - - +
119F ASP* 5.1 0.7 - - - -
122F VAL* 3.7 20.4 - - + -
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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