Contacts of the strand formed by residues 1250 - 1254 (chain A) in PDB entry 4YKN
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 TYR1250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221A ILE* 3.7 8.3 - - + +
1245A GLU* 6.3 0.4 - - - -
1246A TYR* 2.9 57.9 + + + +
1247A GLN 3.4 15.9 - - - +
1248A GLY 3.5 0.8 + - - -
1249A LYS* 1.3 106.5 + - + +
1251A ILE* 1.3 69.4 + - - +
1287A LEU* 3.7 30.1 - - + -
1288A MET* 3.2 24.5 - - - +
1289A ALA* 3.4 21.5 - - + -
1290A LYS* 3.5 2.9 - - - -
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Residues in contact with ILE1251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221A ILE* 4.0 7.6 - - - -
1250A TYR* 1.3 78.3 - - - +
1252A LEU* 1.3 66.4 + - - +
1260A TYR* 3.6 33.4 - - + -
1261A PHE 4.1 17.0 - - - +
1262A LEU* 4.2 19.5 - - + -
1287A LEU* 3.8 5.9 - - - +
1288A MET* 2.9 44.8 + - + +
1290A LYS* 3.8 30.7 - - + -
1293A LEU* 4.5 10.1 - - + -
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Residues in contact with LEU1252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194A ILE* 4.2 25.6 - - + -
1217A PRO* 3.8 28.9 - - + +
1220A VAL* 3.9 20.6 - - + -
1221A ILE* 3.9 22.9 - - + +
1251A ILE* 1.3 77.7 - - - +
1253A LYS* 1.3 59.9 + - - +
1260A TYR* 3.5 6.6 - - - +
1261A PHE* 3.1 54.1 + - + -
1267A LEU* 4.8 0.4 - - + -
1285A LEU* 3.9 17.9 - - + -
1286A MET 3.7 5.8 - - - +
1287A LEU* 4.1 13.7 - - + -
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Residues in contact with LYS1253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252A LEU* 1.3 75.7 - - - +
1254A VAL* 1.3 71.1 + - - +
1255A CYS* 4.6 1.6 - - - +
1256A GLY 4.3 5.1 - - - +
1257A CYS 2.4 33.4 + - - +
1258A ASP* 4.0 8.7 + - - -
1259A GLU 3.4 14.1 - - - +
1260A TYR* 3.6 32.3 - - + +
1261A PHE* 5.5 0.7 - - - -
1285A LEU* 3.2 5.9 - - - -
1286A MET* 2.6 55.0 + - + +
1288A MET* 3.5 32.8 - - + -
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Residues in contact with VAL1254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253A LYS* 1.3 91.3 + - - +
1255A CYS* 1.3 76.5 + - - +
1257A CYS* 3.2 20.5 - - - +
1259A GLU* 3.1 28.4 + - + +
1261A PHE* 3.8 24.0 - - + -
1272A TYR* 3.5 57.0 - - + -
1284A ASN 3.9 4.5 - - - -
1285A LEU* 4.4 1.3 - - + -
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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