Contacts of the strand formed by residues 223 - 225 (chain 2) in PDB entry 1AR9
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 LYS 223 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2091 TYR* 4.0 5.6 - - - +
2111 GLY* 3.1 3.5 - - - -
2121 PHE* 2.8 53.0 + - - +
2131 SER* 2.8 26.0 + - - +
2141 LYS* 4.1 3.8 - - - +
2151 VAL* 3.5 30.7 - - + +
1002 TYR* 6.0 5.7 - - - -
1452 TYR* 4.6 6.1 - - - -
2202 SER* 2.9 30.1 + - - +
2222 VAL* 1.3 76.1 - - - +
2242 HIS* 1.3 58.1 - - - +
2252 ASN* 5.8 0.4 + - - -
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Residues in contact with HIS 224 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2091 TYR* 3.4 30.4 - + - +
2101 ASP 3.1 29.2 - - - -
2111 GLY* 4.1 0.2 - - - -
832 PRO* 3.8 8.0 - - - +
1292 GLU* 2.7 37.7 + - - -
2142 ASN* 3.5 23.4 + - - -
2192 ASP* 2.9 23.9 + - - +
2202 SER 2.9 16.6 + - - +
2212 MET* 3.4 15.2 - - - +
2222 VAL 3.5 1.6 - - - -
2232 LYS* 1.3 81.4 - - + +
2252 ASN* 1.3 77.6 + - - +
2262 ASN* 3.9 12.8 + - - +
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Residues in contact with ASN 225 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2101 ASP* 2.9 42.6 + - - +
2111 GLY* 4.7 0.8 - - - -
812 LYS* 3.5 26.3 - - + +
822 LEU 3.3 10.1 - - - +
832 PRO* 3.3 2.9 - - - +
842 ASP* 3.0 29.1 + - - +
1292 GLU* 3.9 0.5 - - - +
1482 ALA 5.0 0.6 + - - -
1492 ASN* 2.9 28.5 + - - +
2212 MET 4.8 1.9 - - - +
2232 LYS 4.4 0.6 + - - -
2242 HIS* 1.3 89.8 + - - +
2262 ASN* 1.3 62.8 + - - +
2272 TRP 4.4 2.0 - - - +
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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
------------------------------------------------------------
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