Contacts of the strand formed by residues 1046 - 1051 (chain R) in PDB entry 1YYL
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 GLU1046 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1098Q PHE* 4.3 1.1 - - - +
1037R VAL* 3.3 5.9 - - - +
1038R ARG* 3.1 70.3 + - + +
1039R GLN* 5.7 0.4 - - - -
1044R GLY 4.8 2.0 - - - +
1045R LEU* 1.3 78.1 - - - +
1047R TRP* 1.3 72.9 + - - +
1048R MET* 3.3 4.3 + - + +
1063R LEU* 5.2 6.4 - - - +
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Residues in contact with TRP1047 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089Q GLN* 4.5 6.8 - - - +
1095Q ARG* 3.8 30.5 - - - -
1096Q TYR* 3.3 73.1 - + + +
1097Q THR* 4.7 1.3 - - - +
1098Q PHE* 3.6 29.7 - + + +
1035R THR* 3.3 26.2 + - + +
1036R TRP 4.2 1.8 - - - -
1037R VAL* 4.4 0.9 - - + -
1046R GLU* 1.3 75.9 - - - +
1048R MET* 1.3 60.4 + - - +
1049R GLY* 3.6 24.5 - - - -
1050R ARG* 3.5 24.0 - - + -
1058R HIS* 4.4 6.3 - - + -
1059R TYR 4.0 14.1 - - - -
1060R ALA* 3.6 22.2 - - + +
1100R LEU* 5.3 3.1 - - + +
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Residues in contact with MET1048 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036R TRP* 2.8 32.0 + - + +
1037R VAL 4.7 0.7 - - - -
1038R ARG* 3.7 31.0 - - + +
1046R GLU* 3.7 13.2 - - + +
1047R TRP* 1.3 74.9 - - - +
1049R GLY* 1.3 57.3 + - - +
1059R TYR* 3.7 5.2 - - - +
1060R ALA 3.1 21.3 + - - -
1063R LEU* 3.5 37.2 - - + +
1067R VAL* 4.2 18.8 - - + -
1069R ILE* 4.8 1.8 - - + -
1080R LEU* 4.6 7.6 - - + -
1082R LEU* 4.3 4.0 - - + -
1090R TYR* 3.4 40.8 - - + -
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Residues in contact with GLY1049 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035R THR* 3.0 23.7 - - - +
1036R TRP 3.2 7.3 + - - -
1047R TRP* 3.6 17.4 - - - -
1048R MET* 1.3 82.3 - - - +
1050R ARG* 1.3 60.8 + - - -
1058R HIS 3.4 13.5 - - - -
1059R TYR* 4.1 0.2 - - - -
1069R ILE* 3.6 15.2 - - - +
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Residues in contact with ARG1050 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094Q TRP* 3.9 18.2 - - - -
1095Q PRO* 5.4 2.4 + - - +
1096Q TYR* 4.1 20.7 + - - -
1033R SER* 3.4 19.7 + - - +
1034R PHE 3.3 13.9 - - - +
1035R THR* 3.8 14.5 + - - +
1047R TRP* 3.5 15.3 - - + +
1049R GLY* 1.3 75.2 - - - +
1051R ILE* 1.3 66.3 + - - +
1052R ILE* 3.9 14.9 - - + +
1057R ALA* 3.3 2.4 - - - -
1058R HIS* 2.9 39.3 + - + +
1069R ILE* 3.8 3.6 - - - +
1095R VAL* 5.7 0.4 - - - +
1097R GLU* 3.3 15.8 + - - -
1100R ASN* 3.0 66.7 + - - +
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Residues in contact with ILE1051 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033R SER* 3.6 5.4 - - - -
1034R PHE* 3.0 38.6 + - + +
1050R ARG* 1.3 74.5 - - - +
1052R ILE* 1.3 80.5 + - + +
1055R ASP* 4.4 14.8 - - - +
1056R VAL 3.3 15.3 - - - +
1057R ALA* 3.6 7.2 - - + +
1069R ILE* 3.4 28.5 - - + +
1070R THR* 3.8 11.4 - - + -
1071R ALA* 3.7 37.2 - - + +
1078R VAL* 4.7 5.4 - - + -
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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