Contacts of the helix formed by residues 145 - 152 (chain X) in PDB entry 3ISE
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 GLY 145 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147M GLU* 4.1 12.6 + - - -
141X ILE 3.2 15.5 + - - -
142X GLN 4.2 2.1 + - - -
143X LYS 3.6 1.8 - - - -
144X VAL* 1.3 84.5 - - - +
146X LEU* 1.3 65.4 + - - -
147X GLU 3.4 3.3 + - - -
148X ASN 3.5 1.2 + - - -
149X TYR* 3.1 17.7 + - - +
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Residues in contact with LEU 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LYS 6.0 0.7 - - - +
82X ASN* 6.2 0.4 - - - +
83X THR* 5.2 4.5 - - - -
84X GLN* 4.8 16.2 - - + +
141X ILE* 3.6 40.3 + - + +
145X GLY* 1.3 72.1 - - - -
147X GLU* 1.3 64.2 + - + +
149X TYR* 3.3 2.7 + - - +
150X LEU* 3.0 57.2 + - + +
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Residues in contact with GLU 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLN 4.2 6.2 - - - +
143A LYS 3.3 26.0 - - - +
144A VAL* 3.6 30.0 - - - +
145A GLY* 4.0 7.1 + - - -
148A ASN* 3.9 7.7 + - - +
145X GLY 3.4 0.6 - - - -
146X LEU* 1.3 80.3 - - + +
148X ASN* 1.3 62.6 + - - +
150X LEU* 3.9 1.5 - - - +
151X GLN* 2.9 27.9 + - - +
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Residues in contact with ASN 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ASN* 3.2 15.2 + - - +
161A K 3.0 16.5 - - - -
147M GLU* 4.0 16.2 + - - +
148M ASN* 3.0 21.5 + - - +
151M GLN* 3.0 34.3 + - + +
144X VAL* 3.1 30.1 + - + +
145X GLY 3.5 1.4 + - - -
146X LEU 3.4 0.4 - - - -
147X GLU* 1.3 78.0 - - - +
149X TYR* 1.3 63.3 + - - +
151X GLN* 3.3 2.1 + - - -
152X SER* 3.0 20.6 + - - -
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Residues in contact with TYR 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154M MET* 3.9 13.2 - - + -
40X LEU* 4.0 16.5 - - + +
83X THR* 4.4 13.7 - - + -
87X LEU* 4.5 2.7 - - + +
137X GLN* 2.6 53.7 + - + +
140X LEU* 4.1 17.7 - - + -
141X ILE* 3.5 33.2 - - + -
144X VAL* 3.9 11.0 - - + +
145X GLY 3.1 17.5 + - - +
146X LEU 3.6 4.0 - - - +
147X GLU 3.2 0.2 - - - -
148X ASN* 1.3 78.2 - - - +
150X LEU* 1.3 69.5 + - + +
152X SER* 3.3 6.8 + - - -
153X HIS* 2.7 54.3 + + - -
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Residues in contact with LEU 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LYS* 4.1 31.9 - - + +
144A VAL* 3.9 13.9 - - + -
37X LEU* 3.3 34.9 - - + +
40X LEU* 4.6 2.9 - - + -
83X THR* 3.5 40.2 - - + +
146X LEU* 3.0 39.0 + - + +
147X GLU 3.9 1.3 - - - +
149X TYR* 1.3 82.8 - - + +
151X GLN* 1.3 69.1 + - - +
153X HIS* 2.8 14.1 + - - -
154X MET 3.4 0.9 + - - -
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Residues in contact with GLN 151 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 3.6 16.0 - - + +
148A ASN* 3.1 36.6 + - + +
151A GLN* 3.0 25.6 + - - +
152A SER* 3.1 23.0 + - - +
161A K 2.7 22.8 - - - -
151M GLN* 3.0 13.8 + - - +
147X GLU 2.9 18.1 + - - +
148X ASN* 3.3 4.1 - - - +
150X LEU* 1.3 76.8 - - - +
152X SER* 1.3 57.3 + - - +
153X HIS 3.1 4.3 + - - -
154X MET* 3.2 26.5 + - - +
155X HIS* 4.8 0.9 + - - -
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Residues in contact with SER 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M GLN* 3.0 35.5 + - - +
154M MET* 4.1 12.5 - - - -
155M HIS* 3.1 33.6 - - - -
39X ARG* 3.7 7.3 + - - -
148X ASN 3.0 9.3 + - - -
149X TYR 3.7 6.1 - - - -
150X LEU 3.1 0.8 - - - -
151X GLN* 1.3 73.6 - - - +
153X HIS* 1.3 64.4 + - - +
154X MET 3.5 0.7 - - - -
155X HIS 4.5 3.5 - - - +
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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