Contacts of the helix formed by residues 141 - 148 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ALA* 4.6 18.8 - - + +
60B ILE* 4.0 23.1 - - + -
61B GLY* 5.0 2.7 - - - -
64B LYS* 4.6 4.3 - - - -
137B VAL* 3.1 28.2 + - + +
138B LYS 3.3 2.2 - - - -
140B PHE* 1.3 98.3 - - + +
142B LYS* 1.3 66.9 + - - +
143B GLY 3.2 3.5 + - - +
144B PRO* 3.8 17.4 - - + -
145B TYR* 3.0 17.8 + - + +
158C GLY 5.7 1.8 - - - +
159C TYR* 4.0 32.8 - - + -
212C ALA 5.9 0.9 - - - +
216C ILE* 5.1 11.7 - - + -
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LYS* 2.7 50.7 + - + +
139B ALA* 4.7 1.7 + - - +
140B PHE 4.0 0.4 - - - -
141B MET* 1.3 70.2 - - - +
143B GLY* 1.3 63.7 + - - +
145B TYR* 3.1 14.6 + - - +
146B ASN* 3.1 39.1 + - - +
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B MET 3.2 3.0 - - - -
142B LYS* 1.3 80.5 - - - +
144B PRO* 1.3 65.1 - - - +
146B ASN* 4.1 2.2 + - - +
147B GLN* 3.2 28.4 + - - +
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Residues in contact with PRO 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ILE* 3.6 9.5 - - + +
64B LYS* 3.8 45.3 - - + -
141B MET* 3.8 24.0 - - + +
143B GLY* 1.3 86.7 - - - +
145B TYR* 1.3 64.1 + - - +
147B GLN* 3.9 7.4 - - + +
148B PHE* 3.1 35.8 + - + +
158C GLY 6.0 2.7 - - - +
159C TYR* 5.6 0.4 - - + -
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Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 4.2 11.4 - - + -
60B ILE* 3.9 21.4 - - + +
134B VAL* 3.5 15.2 - - + +
137B VAL* 4.2 10.5 - - + -
138B LYS* 3.3 36.8 - - + -
141B MET* 3.0 26.1 + - + +
142B LYS* 3.1 6.0 + - - +
144B PRO* 1.3 77.4 - - - +
146B ASN* 1.3 80.8 + - - +
148B PHE 3.5 1.2 + - - -
150B GLY* 3.0 64.9 + - - -
229B ALA 4.1 0.2 + - - -
232B ILE* 3.5 19.1 - - + +
233B PHE* 3.5 24.9 + + - +
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Residues in contact with ASN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LYS* 3.7 15.8 + - - -
142B LYS* 3.1 46.7 + - - +
143B GLY* 4.6 2.4 + - - +
145B TYR* 1.3 90.4 - - - +
147B GLN* 1.3 64.3 + - - +
148B PHE 3.1 1.7 + - - -
149B GLY 3.6 2.6 + - - -
232B ILE 5.4 0.2 - - - +
233B PHE* 3.5 33.3 - - + +
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLY 3.2 23.4 + - - +
144B PRO* 4.0 9.7 - - + +
145B TYR 3.3 0.4 - - - -
146B ASN* 1.3 80.2 - - - +
148B PHE* 1.3 86.4 + - + +
149B GLY 3.7 1.1 + - - -
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 5.2 3.5 - - - +
60B ILE* 4.2 10.4 - - + +
63B SER* 3.5 44.9 + - - -
64B LYS* 3.6 27.6 - - + -
144B PRO* 3.1 34.1 + - + +
145B TYR 4.1 0.7 - - - -
146B ASN 3.1 0.6 + - - -
147B GLN* 1.3 108.9 - - + +
149B GLY* 1.3 56.6 + - - +
150B GLY 3.3 7.8 + - - -
151B GLY 4.3 1.4 + - - -
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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