Contacts of the helix formed by residues 145 - 152 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147J GLU* 5.6 1.8 - - - -
141Q ILE 2.8 19.2 + - - -
142Q GLN 4.0 3.0 + - - -
143Q LYS 3.7 1.0 - - - -
144Q VAL* 1.3 84.0 - - - +
146Q LEU* 1.3 59.6 + - - -
147Q GLU 3.5 2.4 + - - -
148Q ASN 3.6 1.1 + - - -
149Q TYR* 3.0 25.9 + - - +
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Residues in contact with LEU 146 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Q ASN* 6.0 4.0 - - - +
83Q THR* 4.8 6.3 - - + -
84Q GLN* 5.2 14.4 - - + +
141Q ILE* 4.0 35.3 + - + +
145Q GLY* 1.3 71.4 - - - -
147Q GLU* 1.3 67.6 + - + +
149Q TYR* 3.2 2.9 + - + +
150Q LEU* 2.9 59.3 + - + +
143V LYS 5.4 1.3 - - - +
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Residues in contact with GLU 147 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145Q GLY 3.5 0.6 - - - -
146Q LEU* 1.3 77.9 - - + +
148Q ASN* 1.3 58.6 + - - +
150Q LEU* 3.3 2.9 + - - +
151Q GLN* 2.9 28.8 + - - +
142V GLN 5.0 2.9 - - - +
143V LYS 4.0 19.2 - - - +
144V VAL* 3.5 32.7 - - - +
145V GLY* 4.0 8.2 + - - -
148V ASN* 3.7 9.2 + - - +
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Residues in contact with ASN 148 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J GLU* 3.7 17.8 + - - +
148J ASN* 3.2 22.0 + - - +
151J GLN* 3.1 30.1 + - - +
144Q VAL* 3.3 31.4 + - + +
145Q GLY 3.6 0.8 + - - -
146Q LEU 3.3 0.4 - - - -
147Q GLU* 1.3 72.8 - - - +
149Q TYR* 1.3 69.2 + - - +
150Q LEU 3.0 2.3 + - - -
151Q GLN 3.1 1.4 + - - -
152Q SER* 3.0 20.1 + - - -
148V ASN* 3.0 21.4 + - - +
161V K 3.5 7.4 - - - -
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Residues in contact with TYR 149 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J MET* 4.0 8.7 - - + -
40Q LEU* 3.9 24.1 - - + +
83Q THR* 4.6 5.8 - - + -
87Q LEU* 4.5 2.1 - - + +
137Q GLN* 2.5 60.3 + - + +
140Q LEU* 4.0 17.5 - - + -
141Q ILE* 3.6 32.3 - - + -
144Q VAL* 3.5 9.5 - - + +
145Q GLY 3.0 15.9 + - - +
146Q LEU 3.6 3.8 - - - +
148Q ASN* 1.3 79.5 - - - +
150Q LEU* 1.3 71.6 + - + +
152Q SER* 3.5 5.6 + - - -
153Q HIS* 2.7 54.1 + + - -
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Residues in contact with LEU 150 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q LEU* 3.2 35.9 - - + +
40Q LEU* 4.7 3.6 - - + -
83Q THR* 3.5 39.0 - - + +
146Q LEU* 2.9 44.4 + - + +
147Q GLU 3.7 3.1 - - - +
149Q TYR* 1.3 79.0 - - + +
151Q GLN* 1.3 68.6 + - - +
152Q SER 3.1 1.6 - - - -
153Q HIS* 3.0 11.7 + - - +
154Q MET* 3.4 1.7 + - - +
143V LYS* 3.6 36.3 - - + +
144V VAL* 3.8 9.9 - - + -
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Residues in contact with GLN 151 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J GLN* 2.9 12.9 + - - +
147Q GLU 2.9 13.4 + - - +
148Q ASN 3.4 7.0 - - - +
150Q LEU* 1.3 76.3 - - - +
152Q SER* 1.3 59.7 + - - +
154Q MET* 3.2 28.9 + - - +
155Q HIS* 4.6 1.4 + - - -
144V VAL* 3.7 11.0 - - + +
148V ASN* 3.0 35.1 + - + +
151V GLN* 2.8 24.8 + - - +
152V SER* 2.5 33.1 + - - +
161V K 2.7 22.2 - - - -
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Residues in contact with SER 152 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J GLN* 3.2 35.6 + - - +
154J MET* 4.1 11.6 - - - -
155J HIS* 3.5 31.4 - - - -
39Q ARG* 3.7 6.8 + - - -
148Q ASN 3.0 5.4 + - - -
149Q TYR 3.7 9.0 - - - -
150Q LEU 3.1 0.4 - - - -
151Q GLN* 1.3 75.0 - - - +
153Q HIS* 1.3 64.6 + - - +
154Q MET 3.4 0.6 + - - -
155Q HIS 4.2 5.1 - - - +
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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