Contacts of the strand formed by residues 200 - 203 (chain 2) 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 CYS 200 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1212 PHE* 3.5 32.8 - - + -
1562 PHE* 3.6 20.0 - - + -
1592 ILE 4.0 3.8 - - - +
1602 THR* 4.0 7.0 - - - -
1992 ASP* 1.3 79.2 - - - +
2012 VAL* 1.3 62.6 + - - +
2112 ASP* 3.0 11.1 - - - +
2122 ILE* 2.7 34.6 + - - +
2142 CYS* 2.0 45.7 - - - -
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Residues in contact with VAL 201 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1562 PHE* 3.4 6.9 - - - -
1572 LEU* 2.9 34.3 + - + +
1592 ILE* 3.6 30.0 + - + +
1682 PHE* 3.5 30.7 - - + -
1812 TRP* 3.9 19.7 - - + -
2002 CYS* 1.3 80.1 - - - +
2022 THR* 1.3 68.8 + - - +
2092 TRP* 3.8 37.2 - - + -
2102 ASN 3.7 3.1 - - - +
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Residues in contact with THR 202 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542 SER* 4.7 2.4 - - - -
1552 ALA 3.1 14.8 - - - +
1562 PHE* 3.8 7.2 - - + -
1572 LEU* 4.5 1.3 - - - -
2012 VAL* 1.3 80.9 - - - +
2032 ILE* 1.3 64.3 + - - +
2042 VAL* 3.7 13.0 + - - +
2092 TRP* 3.2 5.7 - - - +
2102 ASN* 3.0 44.4 + - - +
2122 ILE* 3.5 28.3 - - + +
2182 HIS* 3.8 28.2 + - + +
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Residues in contact with ILE 203 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382 PRO* 5.6 0.4 - - + -
1442 ASN* 3.4 46.9 - - - +
1472 ILE* 4.2 15.9 - - + -
1482 GLN* 3.8 19.7 - - + +
1512 ALA* 5.1 1.3 - - + -
1532 THR 3.9 2.7 - - - +
1542 SER* 3.2 4.2 - - - -
1552 ALA* 2.9 41.6 + - + +
1572 LEU* 4.0 25.8 - - + +
2022 THR* 1.3 72.5 - - - +
2042 VAL* 1.3 61.3 + - - +
2072 GLY* 3.4 23.1 - - - +
2082 LEU 3.4 3.4 - - - -
2092 TRP* 4.2 5.2 - - + +
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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