Contacts of the helix formed by residues 140 - 146 (chain D) in PDB entry 3A0B
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 PRO 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471B ALA* 3.5 26.5 - - + +
475B PHE* 3.3 31.4 - - + -
478B VAL* 5.4 0.2 - - + -
479B PHE* 4.2 19.1 - - + -
130D PHE* 3.3 28.0 - - + -
133D ALA* 5.0 3.4 - - + -
138D VAL 3.4 0.2 - - - -
139D ARG* 1.3 82.6 - - + +
141D TYR* 1.3 64.0 + - + +
142D ASN* 3.2 4.0 + - + -
143D ALA* 3.6 4.7 + - + +
144D ILE* 3.0 30.1 + - + +
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Residues in contact with TYR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 2.7 23.6 + - - +
220A THR* 3.3 34.8 - - + -
221A SER* 4.0 13.9 - - - -
468B TRP* 4.0 19.7 - + - -
479B PHE* 3.6 20.8 - + - -
1060B MGE 3.2 37.5 + - - -
139D ARG* 2.6 53.5 + - + -
140D PRO* 1.3 80.3 - - + +
142D ASN* 1.3 58.8 + - - +
144D ILE* 3.1 28.9 - - + +
145D ALA* 3.2 5.2 + - - +
272D LEU* 4.1 9.6 - - + +
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Residues in contact with ASN 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A MET* 4.1 6.0 - - - -
217A SER* 2.8 14.9 + - - +
218A LEU* 4.5 9.6 - - + +
221A SER* 4.1 4.4 + - - +
254A TYR* 2.8 41.1 + - + +
255A PHE* 5.5 0.5 - - - -
258A LEU* 3.3 20.4 - - - +
1039A PHO 2.9 22.8 + - - +
129D GLN* 2.8 27.8 + - - +
140D PRO 3.2 1.6 - - - -
141D TYR* 1.3 74.1 - - - +
143D ALA* 1.3 57.5 - - - +
145D ALA* 2.6 32.7 + - - +
146D PHE 3.2 3.3 + - - -
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TYR* 4.0 0.4 + - - -
126D MET* 3.3 24.4 - - + +
129D GLN* 3.0 38.0 - - + +
130D PHE* 3.7 33.2 - - + +
140D PRO* 3.6 2.8 + - + +
142D ASN* 1.3 79.3 - - - +
144D ILE* 1.3 62.6 + - - +
146D PHE* 2.9 18.4 + - - +
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Residues in contact with ILE 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B PHE* 4.4 12.9 - - + -
467B ILE* 3.4 22.4 - - + +
468B TRP* 3.4 52.3 - - + -
471B ALA* 4.2 9.9 - - + -
1060B MGE 5.2 7.3 - - + +
130D PHE* 4.8 0.8 - - + -
140D PRO* 3.0 16.8 + - + +
141D TYR* 3.1 32.1 - - + +
143D ALA* 1.3 74.5 - - - +
145D ALA* 1.3 64.1 + - + +
146D PHE 3.0 5.5 + - - -
147D SER* 3.0 26.9 + - - -
272D LEU* 4.4 12.3 - - + -
276D VAL* 4.7 1.0 - - - +
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ALA 4.2 5.4 - - - +
217A SER* 3.8 6.1 - - - +
1039A PHO 4.2 15.4 - - + +
141D TYR 3.2 5.6 - - - +
142D ASN 2.6 17.7 + - - +
144D ILE* 1.3 78.1 - - - +
146D PHE* 1.3 55.8 + - - -
147D SER 3.2 1.9 + - - -
148D ALA 3.7 1.0 + - - -
149D PRO* 3.4 9.9 - - - +
272D LEU* 3.1 33.2 - - + -
276D VAL* 3.4 24.9 - - + +
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Residues in contact with PHE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039A PHO 3.5 54.0 - + - -
122D LEU* 3.4 31.9 - - + -
125D PHE* 3.3 29.6 - + - -
126D MET* 3.4 26.0 - - + -
129D GLN* 3.3 13.7 - - - +
142D ASN 3.2 2.2 + - - -
143D ALA 2.9 16.1 + - - +
145D ALA* 1.3 74.7 - - - +
147D SER* 1.3 61.6 + - - +
149D PRO* 2.7 38.8 - - + +
150D ILE* 3.0 22.1 + - + +
1004D CLA 4.8 4.5 - - + -
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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