Contacts of the helix formed by residues 138 - 146 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ASN* 4.1 9.7 + - - +
150D CYS* 3.1 21.6 - - - -
98E ASN 5.4 0.2 - - - +
99E GLY* 3.3 15.4 - - - +
100E TYR* 3.8 21.3 + - + -
136E GLN 3.7 4.0 + - - -
137E VAL* 1.3 71.0 - - - +
139E TYR* 1.3 66.5 + - - +
140E GLU* 2.9 42.8 + - - +
141E GLU* 2.8 45.2 + - - +
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Residues in contact with TYR 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E ARG* 3.5 47.6 + - + +
90E PHE* 3.5 49.8 - + + -
91E ARG* 5.2 6.7 - - - +
94E ASP* 3.7 14.4 + - - -
99E GLY* 3.4 35.7 - - - -
101E ILE* 5.3 5.2 - - + -
137E VAL* 3.3 14.6 + - + +
138E ASN* 1.3 72.0 - - - +
140E GLU* 1.3 73.5 + - - +
142E PHE* 3.1 7.7 + - - +
143E VAL* 3.0 30.7 + - - +
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Residues in contact with GLU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ASN* 4.8 1.2 - - - +
82D TYR* 3.5 21.6 + - - -
83D ASN* 5.1 4.7 + - - -
150D CYS* 3.3 16.8 - - - -
151D CYS* 5.9 0.2 - - - -
87E ARG* 4.5 14.7 - - - +
98E ASN 5.8 0.3 - - - +
99E GLY* 5.8 0.6 - - - -
138E ASN* 2.9 36.3 + - - +
139E TYR* 1.3 96.9 + - + +
141E GLU* 1.3 60.5 + - - +
143E VAL* 3.6 8.7 - - - -
144E GLN* 2.9 50.2 + - - +
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Residues in contact with GLU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D CYS* 4.3 17.5 - - - +
152D CYS* 4.5 5.6 - - + +
129E ALA 2.9 24.8 - - - +
130E ASP* 3.8 5.9 - - - +
131E ILE* 3.1 33.5 + - + +
132E ASP* 4.6 4.0 - - - +
138E ASN* 2.8 40.6 + - + +
140E GLU* 1.3 82.2 - - - +
142E PHE* 1.3 58.7 + - - +
144E GLN* 3.8 3.3 - - - -
145E MET* 3.0 30.4 + - - +
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Residues in contact with PHE 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D ILE* 5.5 6.5 - - + -
344D TRP* 3.9 19.7 - + - -
86E ILE* 6.0 4.0 - - + -
90E PHE* 4.2 24.5 - + - -
125E MET* 4.7 5.2 - - + -
128E GLU* 3.3 32.1 - - + -
129E ALA* 3.4 32.5 - - + +
131E ILE* 5.6 0.2 - - - -
137E VAL* 5.1 0.2 - - + -
139E TYR* 3.1 14.6 + - - +
141E GLU* 1.3 84.0 - - - +
143E VAL* 1.3 58.7 + - + +
145E MET* 3.3 6.6 + - + +
146E MET* 3.0 69.8 + - + +
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Residues in contact with VAL 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E GLU* 3.2 24.3 - - - +
86E ILE* 3.5 34.1 - - + -
87E ARG* 3.6 15.3 - - + -
90E PHE* 3.6 27.6 - - + -
139E TYR 3.0 15.5 + - - +
140E GLU* 3.3 18.6 - - - +
142E PHE* 1.3 79.0 - - + +
144E GLN* 1.3 62.1 + - + +
147E THR* 3.0 36.1 + - - -
148E ALA 3.4 1.6 + - - -
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Residues in contact with GLN 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D TYR* 5.5 4.0 + - - -
150D CYS 4.3 0.3 - - - +
151D CYS* 2.6 47.4 - - - -
152D CYS* 3.3 28.7 + - + +
153D ARG* 4.2 19.5 + - + +
83E GLU* 3.5 20.6 - - - +
87E ARG* 4.5 9.5 - - - +
140E GLU* 2.9 38.0 + - - +
141E GLU 4.3 0.3 + - - -
143E VAL* 1.3 75.1 - - + +
145E MET* 1.3 60.9 + - - +
148E ALA* 3.9 15.9 - - - +
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Residues in contact with MET 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D CYS* 3.9 15.9 - - - -
347D TYR* 5.6 0.7 - - - -
353D ARG* 4.8 5.4 - - - +
128E GLU* 3.2 46.9 - - - +
131E ILE* 3.8 17.7 - - + -
141E GLU 3.0 18.8 + - - +
142E PHE* 3.6 4.9 - - + +
143E VAL 3.2 0.2 - - - -
144E GLN* 1.3 81.3 - - - +
146E MET* 1.3 86.7 + - + +
148E ALA 4.6 6.1 + - - +
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Residues in contact with MET 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D ALA* 5.4 1.3 - - + +
344D TRP* 4.5 3.6 - - + -
347D TYR* 3.4 63.3 - - + -
76E LYS* 6.0 0.2 + - - -
77E MET* 3.8 26.6 - - + +
128E GLU* 3.9 3.6 - - - +
142E PHE* 3.0 50.3 + - + +
145E MET* 1.3 92.2 - - - +
147E THR* 1.3 67.3 + - - +
148E ALA 2.9 13.3 - - - +
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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