Contacts of the helix formed by residues 137 - 142 (chain E) in PDB entry 3SHD
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 PRO 137 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D TYR* 4.0 20.6 - - + +
64E HIS* 5.7 2.7 - - + -
65E PHE* 3.8 4.9 - - - +
135E ARG 4.3 2.7 - - - +
136E TYR* 1.3 97.1 - - + +
138E LEU* 1.3 64.2 + - - +
139E GLU* 3.6 19.7 - - + +
140E MET* 3.1 23.6 + - + +
13F HIS* 6.0 1.1 - - - +
130F TYR* 6.0 6.3 - - + -
133F GLY* 6.1 1.1 - - - -
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Residues in contact with LEU 138 (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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45E VAL* 4.4 19.3 - - + +
61E GLN* 6.2 0.9 - - + -
62E PRO* 3.5 26.9 - - + +
63E GLN* 3.6 17.6 + - - +
64E HIS* 3.5 28.9 - - - +
65E PHE* 3.7 4.3 - - - +
84E PHE* 3.7 24.7 - - + -
136E TYR 3.5 1.0 + - - -
137E PRO* 1.3 66.7 - - - +
139E GLU* 1.3 72.1 + - - +
140E MET 2.9 10.9 + - - -
141E ILE* 3.2 22.6 + - - +
142E GLY* 3.8 4.3 + - - -
87F GLU* 5.9 0.9 - - - +
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Residues in contact with GLU 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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67D ARG* 3.3 30.5 + - - +
137E PRO* 3.6 14.7 - - + +
138E LEU* 1.3 96.8 + - - +
140E MET* 1.3 61.0 + - - +
141E ILE 3.1 1.3 + - - -
142E GLY* 3.3 7.9 + - - +
13F HIS* 3.9 22.4 + - - -
15F GLU* 5.2 5.2 + - - -
16F GLY* 4.9 16.0 + - - +
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Residues in contact with MET 140 (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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65D PHE* 3.2 30.5 - - + -
66D ILE 4.7 0.2 - - - +
67D ARG* 3.3 11.4 - - + +
68D MET 3.1 22.7 + - - -
134D GLN* 5.4 1.6 - - - -
136D TYR* 3.2 50.0 - - + +
140D MET* 3.5 20.2 - - + +
65E PHE* 3.3 36.1 - - + -
136E TYR* 4.5 7.9 - - - -
137E PRO* 3.1 22.1 + - + +
138E LEU 2.9 1.6 - - - -
139E GLU* 1.3 79.5 - - - +
141E ILE* 1.3 66.2 + - + +
142E GLY 3.6 0.2 - - - -
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Residues in contact with ILE 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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65D PHE* 5.0 3.1 - - + -
68D MET* 3.1 40.8 - - + +
70D GLN* 4.6 1.7 - - - +
141D ILE* 5.2 2.7 - - + -
44E LEU* 3.8 30.1 - - + +
45E VAL* 4.8 6.3 - - + -
65E PHE* 4.0 43.7 - - + -
82E PHE* 4.1 13.0 - - + -
84E PHE* 4.0 21.1 - - + -
138E LEU 3.2 13.6 + - - +
139E GLU 3.1 0.2 - - - -
140E MET* 1.3 91.6 - - + +
142E GLY* 1.3 58.1 + - - +
143E ASP 4.0 0.3 + - - -
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Residues in contact with GLY 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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67D ARG* 2.4 35.0 + - - +
69D HIS* 3.7 0.2 - - - -
70D GLN* 3.0 18.0 + - - -
138E LEU 4.2 5.8 - - - -
139E GLU* 3.3 9.6 + - - -
141E ILE* 1.3 79.8 - - - +
143E ASP* 1.3 66.1 + - - -
144E PHE 3.7 0.2 + - - -
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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