Contacts of the helix formed by residues 141 - 148 (chain C) in PDB entry 4IA4
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 MET 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A TYR* 4.0 27.6 - - + -
212A ALA 5.7 0.2 - - - +
216A ILE* 4.1 21.5 - - + -
53C TYR* 5.6 0.4 - - + -
57C ALA* 4.5 15.3 - - + +
60C ILE* 3.8 27.8 - - + -
61C GLY* 5.1 2.2 - - - -
64C LYS* 5.1 0.7 - - - -
137C VAL* 3.0 33.4 + - + +
138C LYS 3.6 2.5 - - - -
140C PHE* 1.3 100.1 - - + +
142C LYS* 1.3 64.2 + - - +
143C GLY 3.4 2.2 - - - -
144C PRO* 3.5 19.7 - - + +
145C TYR* 3.0 18.7 + - + +
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Residues in contact with LYS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LYS* 3.0 37.0 + - + +
139C ALA 5.0 0.4 - - - -
140C PHE 4.0 0.6 - - - -
141C MET* 1.3 68.0 - - - +
143C GLY* 1.3 72.2 + - - +
145C TYR* 4.0 4.3 - - - -
146C ASN* 3.0 46.7 + - - +
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Residues in contact with GLY 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C MET 3.4 0.2 - - - -
142C LYS* 1.3 83.0 - - - +
144C PRO* 1.3 64.2 - - - +
146C ASN* 3.1 2.6 + - - +
147C GLN* 2.9 29.0 + - - +
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Residues in contact with PRO 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TYR* 5.7 0.4 - - + -
60C ILE* 4.0 9.3 - - + +
64C LYS* 3.9 39.5 - - + -
141C MET* 3.5 29.6 - - + +
143C GLY* 1.3 83.8 - - - +
145C TYR* 1.3 67.2 + - - +
147C GLN* 3.9 8.4 - - + +
148C PHE* 2.9 39.7 + - + +
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Residues in contact with TYR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C VAL* 4.3 7.6 - - + -
60C ILE* 4.1 21.2 - - + +
134C VAL* 3.3 28.2 - - + +
137C VAL* 4.6 3.8 - - + -
138C LYS* 3.4 46.7 - - + -
141C MET* 3.0 26.8 + - + +
142C LYS* 3.3 6.3 - - - +
143C GLY 3.1 0.2 - - - -
144C PRO* 1.3 81.0 - - - +
146C ASN* 1.3 72.1 - - - +
148C PHE 3.6 1.9 + - - -
150C GLY* 2.9 64.9 + - - -
229C ALA 4.0 0.5 + - - -
232C ILE* 3.8 2.9 - - + +
233C PHE* 3.5 29.1 + + - +
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Residues in contact with ASN 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LYS* 3.6 21.1 + - - +
142C LYS* 3.0 44.8 + - - +
143C GLY 3.9 1.3 - - - +
145C TYR* 1.3 87.1 - - - +
147C GLN* 1.3 66.4 + - - +
148C PHE 3.1 3.2 + - - -
149C GLY 3.9 2.6 + - - -
233C PHE* 3.8 34.5 - - + +
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Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C GLY 2.9 15.1 + - - +
144C PRO* 3.3 13.5 + - + +
146C ASN* 1.3 77.6 - - - +
148C PHE* 1.3 93.9 + - + +
149C GLY 3.9 1.1 + - - -
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Residues in contact with PHE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C VAL* 5.6 2.4 - - - +
60C ILE* 4.1 13.0 - - + +
63C SER* 3.5 43.6 + - - -
64C LYS* 3.4 32.8 - - + -
144C PRO* 2.9 30.7 + - + +
145C TYR 4.0 0.7 - - - -
146C ASN 3.1 0.8 - - - -
147C GLN* 1.3 115.8 - - + +
149C GLY* 1.3 55.2 + - - +
150C GLY 3.2 9.1 + - - -
151C GLY* 4.2 1.7 + - - -
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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