Contacts of the strand formed by residues 209 - 212 (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 TRP 209 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1381 PRO* 3.5 25.4 - - + -
1441 ASN* 2.9 19.6 + - - -
1571 LEU* 3.7 17.8 - - + +
1591 ILE* 3.6 25.1 - - + -
1701 TYR* 6.1 0.2 - + - -
1761 LEU* 4.1 12.6 - - + -
1781 TYR* 3.4 36.3 - + - -
1791 SER* 3.6 13.2 - - - -
1801 ASN* 2.7 29.6 + - - +
1811 TRP* 3.6 28.4 - + + -
1821 LYS* 2.9 33.6 + - - +
1851 GLN* 3.9 1.0 - - - +
2011 VAL* 3.9 16.4 - - + -
2021 THR 3.4 6.1 - - - +
2031 ILE* 4.3 5.4 - - - +
2041 VAL* 5.2 0.2 - - - -
2071 GLY 3.5 7.6 - - - -
2081 LEU* 1.3 82.7 - - - +
2101 ASN* 1.3 61.3 + - - +
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Residues in contact with ASN 210 (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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11 NGA 3.0 49.6 + - - +
21 CA 2.4 24.8 - - - -
1811 TRP* 4.1 4.5 - - - -
1821 LYS* 4.8 5.4 - - + -
1851 GLN* 2.9 22.5 - - + +
2011 VAL* 3.5 0.3 - - - -
2021 THR* 3.0 39.8 + - - +
2041 VAL* 4.4 11.7 - - + -
2081 LEU 4.4 0.2 + - - -
2091 TRP* 1.3 76.7 - - - +
2111 ASP* 1.3 65.9 + - - +
2121 ILE* 3.8 9.7 - - - +
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Residues in contact with ASP 211 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 NGA 3.1 2.9 + - - -
21 CA 2.2 52.3 - - - -
1681 PHE* 4.0 14.8 - - + -
1811 TRP* 3.8 6.6 - - + -
1851 GLN* 3.0 9.0 - - - +
1861 PRO* 3.3 23.0 - - + +
1871 ASP* 3.1 5.5 + - - +
1881 ASP* 2.7 30.7 + - - +
1981 GLU* 2.8 17.0 - - + +
2001 CYS 3.0 12.8 - - - +
2011 VAL* 4.2 1.8 - - - +
2101 ASN* 1.3 77.5 + - - +
2121 ILE* 1.3 58.3 + - - +
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Residues in contact with ILE 212 (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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11 NGA 3.8 26.9 - - + +
1561 PHE* 3.8 11.7 - - + -
1891 TRP* 5.9 1.1 - - + -
1921 HIS* 6.1 3.4 - - + -
1981 GLU* 3.5 24.2 - - - +
1991 ASP 3.4 2.9 + - - -
2001 CYS* 2.8 32.4 + - - +
2021 THR* 3.6 31.6 - - + +
2101 ASN* 3.8 12.6 - - - +
2111 ASP* 1.3 72.8 - - - +
2131 SER* 1.3 78.9 + - - +
2161 ALA* 4.1 9.4 - - + -
2181 HIS* 3.9 19.3 - - + +
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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