Contacts of the helix formed by residues 141 - 151 (chain 1) in PDB entry 1AFB
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 ALA 141 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1401 ASN* 1.3 74.9 - - - +
1421 GLU* 1.3 56.9 - - - +
1441 ASN* 3.4 2.9 + - - +
1451 LYS* 2.9 29.9 + - - +
1781 TYR* 3.7 20.0 - - + +
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Residues in contact with GLU 142 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091 LYS* 3.2 45.6 + - - +
1401 ASN* 3.0 16.1 + - - +
1411 ALA* 1.3 78.6 - - - +
1431 GLU* 1.3 62.0 + - - +
1451 LYS* 3.3 7.2 + - - +
1461 ALA* 3.0 27.8 + - + +
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Residues in contact with GLU 143 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101 LYS* 3.2 50.1 + - + +
1121 PHE* 4.1 7.6 - - + -
1371 ILE 3.5 5.9 - - - +
1381 PRO* 3.9 11.0 - - + -
1391 ARG* 2.9 26.0 + - - +
1401 ASN* 2.9 33.3 + - - +
1421 GLU* 1.3 76.1 - - + +
1441 ASN* 1.3 66.5 + - - +
1461 ALA* 3.1 7.9 + - - +
1471 ILE* 2.9 27.7 + - - +
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Residues in contact with ASN 144 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381 PRO* 3.4 20.9 - - + +
1401 ASN 3.0 16.9 + - - +
1411 ALA 3.5 5.4 - - - +
1431 GLU* 1.3 76.9 - - - +
1451 LYS* 1.3 60.3 + - - +
1471 ILE* 3.4 1.4 + - - +
1481 GLN* 3.0 30.1 + - - +
1781 TYR* 3.6 15.2 + - - +
1801 ASN* 3.5 9.4 - - - +
2031 ILE* 3.5 14.0 - - - +
2071 GLY* 2.9 28.9 + - - -
2091 TRP* 2.9 28.4 + - - -
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Residues in contact with LYS 145 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1411 ALA 2.9 17.5 + - - +
1421 GLU* 3.5 7.9 - - - +
1441 ASN* 1.3 75.8 - - - +
1461 ALA* 1.3 58.3 + - - +
1481 GLN* 3.3 36.8 + - - +
1491 GLU* 2.9 66.9 + - - +
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Residues in contact with ALA 146 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121 PHE* 3.9 21.3 - - + -
1421 GLU* 3.0 15.7 + - + +
1431 GLU* 3.1 9.6 + - - +
1451 LYS* 1.3 74.5 - - - +
1471 ILE* 1.3 65.0 + - - +
1491 GLU* 3.3 9.7 + - - +
1501 VAL* 3.0 29.5 + - + +
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Residues in contact with ILE 147 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121 PHE* 3.5 36.3 - - + -
1361 ALA* 3.8 16.8 - - + -
1381 PRO* 3.5 47.3 - - + -
1431 GLU 2.9 13.6 + - - +
1441 ASN 3.8 3.4 - - - +
1461 ALA* 1.3 73.4 - - - +
1481 GLN* 1.3 64.5 + - - +
1501 VAL* 3.0 7.2 + - - +
1511 ALA* 2.9 25.3 + - + +
1551 ALA* 5.3 1.1 - - + -
1571 LEU* 4.2 7.4 - - + -
2031 ILE* 4.0 23.3 - - + -
2211 VAL* 4.4 11.9 - - + -
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Residues in contact with GLN 148 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1441 ASN* 3.0 17.4 + - - +
1451 LYS* 3.3 43.7 + - - +
1471 ILE* 1.3 77.3 - - - +
1491 GLU* 1.3 58.4 + - + +
1511 ALA* 5.0 2.7 - - - -
1521 LYS* 2.9 30.0 + - - +
1531 THR 4.7 1.1 + - - +
2031 ILE* 3.8 17.4 - - + +
2041 VAL 4.8 1.1 - - - +
2051 ASP 2.9 27.3 - - - +
2061 ASN* 3.3 12.4 + - - +
2071 GLY* 3.8 17.2 - - - +
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Residues in contact with GLU 149 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1451 LYS* 2.9 60.0 + - - +
1461 ALA* 3.7 7.4 + - - +
1471 ILE 3.2 0.2 - - - -
1481 GLN* 1.3 75.4 - - + +
1501 VAL* 1.3 63.2 + - + +
1521 LYS* 3.1 29.8 - - - +
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Residues in contact with VAL 150 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031 MET 6.0 1.1 - - - +
1121 PHE* 3.6 44.2 - - + +
1131 VAL* 4.1 6.3 - - - +
1141 THR* 3.7 27.4 - - + +
1161 HIS* 3.8 9.0 - - - -
1461 ALA* 3.0 20.7 + - + +
1471 ILE* 3.0 3.8 + - - +
1491 GLU* 1.3 80.2 - - + +
1511 ALA* 1.3 62.9 + - - +
1521 LYS* 4.0 4.9 + - - +
2211 VAL* 4.1 9.0 - - + -
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Residues in contact with ALA 151 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141 THR* 4.6 4.0 - - - -
1161 HIS* 4.2 12.3 + - - -
1471 ILE* 2.9 20.9 + - + +
1481 GLN* 4.3 2.5 - - - +
1501 VAL* 1.3 73.7 - - - +
1521 LYS* 1.3 72.5 + - - +
1531 THR* 3.1 27.9 + - - +
1551 ALA* 3.8 11.9 - - + -
2031 ILE* 5.2 1.1 - - + -
2191 THR* 4.7 4.6 - - + +
2211 VAL* 3.7 26.5 - - + -
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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