Contacts of the helix formed by residues 145 - 152 (chain O) in PDB entry 3IS7
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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141O ILE 2.9 16.2 + - - -
142O GLN 4.1 1.7 + - - -
143O LYS 3.6 1.4 - - - -
144O VAL* 1.3 84.0 - - - +
146O LEU* 1.3 66.6 + - - -
147O GLU 3.4 2.6 + - - -
148O ASN 3.5 0.4 + - - -
149O TYR* 3.0 19.6 + - - +
147W GLU* 3.9 16.2 + - - -
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Residues in contact with LEU 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I LYS 5.6 0.9 - - - +
83O THR* 5.2 4.5 - - - -
84O GLN* 4.6 19.1 - - + +
141O ILE* 3.6 39.8 + - + +
145O GLY* 1.3 71.2 - - - -
147O GLU* 1.3 61.0 + - + +
149O TYR* 3.7 2.6 - - + +
150O LEU* 3.0 61.1 + - + +
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Residues in contact with GLU 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I GLN 4.7 4.7 - - - +
143I LYS 3.6 22.6 - - - +
144I VAL* 3.4 23.0 - - - +
145I GLY* 3.8 15.8 + - - -
148I ASN* 3.7 8.7 + - - +
145O GLY 3.4 1.0 - - - -
146O LEU* 1.3 78.2 - - + +
148O ASN* 1.3 59.2 + - - +
150O LEU* 3.5 2.1 + - - +
151O GLN* 3.0 28.1 + - - +
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Residues in contact with ASN 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G K 3.0 17.7 - - - -
148I ASN* 3.0 15.9 + - - +
144O VAL* 3.3 29.7 + - + +
145O GLY 3.5 1.4 + - - -
146O LEU 3.4 0.2 - - - -
147O GLU* 1.3 74.5 - - - +
149O TYR* 1.3 68.4 + - - +
151O GLN* 3.1 1.1 + - - -
152O SER* 2.9 22.5 + - - -
147W GLU* 3.5 23.3 + - - +
148W ASN* 3.1 20.0 + - - +
151W GLN* 3.1 29.0 + - - +
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Residues in contact with TYR 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O LEU* 3.9 25.2 - - + +
83O THR* 4.2 6.3 - - + -
87O LEU* 4.2 1.6 - - + +
137O GLN* 2.6 55.0 + - + +
140O LEU* 3.9 28.3 - - + -
141O ILE* 3.5 33.0 - - + -
144O VAL* 3.7 11.1 - - + +
145O GLY 3.0 17.9 + - - +
146O LEU* 3.7 4.5 - - + +
147O GLU 3.3 0.2 - - - -
148O ASN* 1.3 77.1 - - - +
150O LEU* 1.3 73.3 + - + +
152O SER* 3.3 7.2 + - - -
153O HIS* 2.9 51.9 + + - -
154W MET* 4.5 4.9 - - + -
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Residues in contact with LEU 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I LYS* 3.7 33.7 - - + +
144I VAL* 3.8 14.6 - - + -
37O LEU* 3.4 35.3 - - + +
40O LEU* 4.6 3.6 - - + -
83O THR* 3.5 41.3 - - + +
146O LEU* 3.0 39.0 + - + +
147O GLU 3.8 0.7 - - - +
149O TYR* 1.3 78.0 - - + +
151O GLN* 1.3 67.2 + - - +
153O HIS* 2.9 11.9 + - - -
154O MET* 3.4 1.9 + - - +
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Residues in contact with GLN 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G K 2.8 21.2 - - - -
144I VAL* 3.6 12.3 - - + +
148I ASN* 3.0 31.6 + - + +
151I GLN* 2.7 28.4 + - - +
152I SER* 3.0 30.7 + - - +
147O GLU 3.0 14.5 + - - +
148O ASN 3.1 6.5 + - - +
150O LEU* 1.3 76.1 - - - +
152O SER* 1.3 59.3 + - - +
153O HIS 3.1 4.7 + - - -
154O MET* 3.2 22.4 + - - +
155O HIS* 4.8 2.3 + - - -
151W GLN* 2.9 14.4 + - - +
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Residues in contact with SER 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O ARG* 3.6 6.8 + - - -
148O ASN 2.9 6.8 + - - -
149O TYR 3.4 11.2 - - - -
150O LEU 3.2 0.2 - - - -
151O GLN* 1.3 76.7 - - - +
153O HIS* 1.3 62.9 + - - +
154O MET 3.5 0.4 - - - -
155O HIS 4.6 2.4 - - - +
151W GLN* 3.0 35.6 + - - +
154W MET* 3.9 21.2 - - - +
155W HIS* 3.3 26.0 - - - -
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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