Contacts of the helix formed by residues 138 - 146 (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 ASN 138 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASN* 4.1 9.8 + - - +
150A CYS* 3.1 21.8 - - - -
98F ASN 5.4 0.3 - - - +
99F GLY* 3.3 15.5 - - - +
100F TYR* 3.8 21.5 + - + -
136F GLN 3.7 4.2 + - - +
137F VAL* 1.3 71.1 - - - +
139F TYR* 1.3 66.1 + - - +
140F GLU* 2.9 43.9 + - - +
141F GLU* 2.8 45.7 + - - +
142F PHE 3.7 0.3 + - - -
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Residues in contact with TYR 139 (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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87F ARG* 3.5 49.2 + - + +
90F PHE* 3.5 50.0 - + + -
91F ARG* 5.2 6.5 - - - +
94F ASP* 3.7 14.7 + - - -
99F GLY* 3.4 35.2 - - - +
101F ILE* 5.3 5.6 - - + -
137F VAL* 3.3 14.8 + - + +
138F ASN* 1.3 72.1 - - - +
140F GLU* 1.3 74.1 + - - +
142F PHE* 3.1 8.0 + - - +
143F VAL* 3.0 30.9 + - + +
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Residues in contact with GLU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN* 4.8 1.0 - - - +
82A TYR* 3.5 21.7 + - - -
83A ASN* 5.1 4.2 + - - -
150A CYS* 3.3 16.9 - - - -
151A CYS* 5.9 0.2 - - - -
87F ARG* 4.5 14.0 - - - +
98F ASN 5.8 0.5 - - - +
99F GLY* 5.8 0.8 - - - -
100F TYR* 5.5 0.2 + - - -
138F ASN* 2.9 36.4 + - - +
139F TYR* 1.3 95.2 + - + +
141F GLU* 1.3 59.8 + - - +
143F VAL* 3.6 9.6 - - - -
144F GLN* 2.9 50.1 + - - +
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Residues in contact with GLU 141 (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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150A CYS* 4.3 17.9 - - - +
152A CYS* 4.5 5.9 - - + +
129F ALA 2.9 22.8 - - - +
130F ASP* 3.8 6.4 - - - +
131F ILE* 3.1 33.0 + - + +
132F ASP* 4.6 4.7 - - - +
138F ASN* 2.8 39.9 + - + +
140F GLU* 1.3 80.4 - - - +
142F PHE* 1.3 58.3 + - - +
144F GLN* 3.8 3.8 - - - +
145F MET* 3.0 30.1 + - - +
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Residues in contact with PHE 142 (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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340A ILE* 5.5 6.3 - - + -
344A TRP* 3.9 19.1 - + + -
86F ILE* 6.0 4.0 - - + -
90F PHE* 4.2 24.7 - + - -
125F MET* 4.7 4.9 - - + -
128F GLU* 3.3 32.3 - - + -
129F ALA* 3.4 33.2 - - + +
138F ASN 3.7 0.4 + - - +
139F TYR* 3.1 13.7 + - - +
141F GLU* 1.3 83.8 - - + +
143F VAL* 1.3 58.4 + - + +
145F MET* 3.3 7.5 + - + +
146F MET* 3.0 70.8 + - + +
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Residues in contact with VAL 143 (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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83F GLU* 3.2 24.5 - - - +
86F ILE* 3.5 33.7 - - + -
87F ARG* 3.6 15.7 - - + -
90F PHE* 3.6 26.9 - - + -
139F TYR* 3.0 15.5 + - + +
140F GLU* 3.3 18.2 - - - +
142F PHE* 1.3 78.6 - - + +
144F GLN* 1.3 60.9 + - + +
147F THR* 3.0 36.0 + - - -
148F ALA 3.4 1.7 + - - -
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Residues in contact with GLN 144 (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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82A TYR* 5.5 3.1 + - - -
150A CYS 4.3 0.2 - - - +
151A CYS* 2.6 48.1 - - - +
152A CYS* 3.3 28.7 + - + +
153A ARG* 4.2 19.3 + - + +
83F GLU* 3.5 20.6 - - - +
87F ARG* 4.5 8.8 - - - +
140F GLU* 2.9 39.4 + - - +
141F GLU 4.3 0.3 + - - -
143F VAL* 1.3 75.3 - - + +
145F MET* 1.3 60.6 + - - +
148F ALA* 3.9 16.2 - - - +
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Residues in contact with MET 145 (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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152A CYS* 3.9 15.3 - - - -
347A TYR* 5.6 0.4 - - - -
353A ARG* 4.8 5.6 - - - +
128F GLU* 3.2 46.9 - - - +
131F ILE* 3.8 17.7 - - + -
141F GLU 3.0 18.8 + - - +
142F PHE* 3.6 5.4 - - + +
143F VAL 3.2 0.4 - - - -
144F GLN* 1.3 81.5 - - - +
146F MET* 1.3 85.2 + - + +
148F ALA 4.6 6.3 - - - +
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Residues in contact with MET 146 (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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343A ALA* 5.4 0.7 - - + +
344A TRP* 4.5 3.1 - - + -
347A TYR* 3.4 63.0 - - + -
76F LYS* 6.0 0.3 + - - -
77F MET* 3.8 25.7 - - + +
128F GLU* 3.9 4.3 - - - -
142F PHE* 3.0 51.6 + - + +
145F MET* 1.3 92.0 - - - +
147F THR* 1.3 69.6 + - - +
148F ALA 2.9 12.5 - - - +
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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