Contacts of the strand formed by residues 1107 - 1111 (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 THR1107 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006R GLU* 2.7 26.1 + - - +
1007R SER* 3.0 23.5 + - - +
1008R GLY 3.0 30.1 - - - +
1010R GLU* 4.7 2.5 - - + -
1020R VAL* 3.7 18.5 - - + +
1089R VAL* 3.1 5.0 - - - +
1090R TYR* 2.7 39.8 + - - -
1106R GLY* 1.3 71.0 - - - -
1108R LEU* 1.3 70.4 + - - +
1109R VAL* 3.8 10.7 + - + +
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Residues in contact with LEU1108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009R ALA* 3.6 17.1 - - + +
1010R GLU 3.1 24.3 + - - +
1041R PRO* 6.0 2.5 - - + -
1087R THR* 5.0 4.7 - - + -
1088R ALA* 3.3 25.4 - - - +
1089R VAL* 3.9 17.2 - - + +
1106R GLY 4.3 0.4 + - - -
1107R THR* 1.3 76.1 - - - +
1109R VAL* 1.3 68.0 + - - +
1110R THR* 4.0 20.6 - - - +
1148R GLU* 4.9 23.8 - - + +
1149R PRO* 5.6 3.1 - - + -
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Residues in contact with VAL1109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010R GLU* 3.6 18.4 - - + -
1012R LYS* 4.5 5.2 - - + -
1018R VAL* 4.1 24.9 - - + -
1020R VAL* 4.5 10.5 - - + -
1082R LEU* 5.2 1.6 - - + -
1086R ASP 5.3 1.1 - - - +
1087R THR* 3.2 7.8 - - - +
1088R ALA 2.8 30.0 + - - -
1090R TYR* 3.4 34.8 - - + -
1107R THR* 4.0 13.2 - - + +
1108R LEU* 1.3 81.4 - - - +
1110R THR* 1.3 60.2 + - - +
1111R VAL* 3.9 16.1 + - + +
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Residues in contact with THR1110 (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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1010R GLU 3.0 12.8 + - - -
1011R VAL* 3.0 35.8 - - - +
1012R LYS 3.0 5.4 + - - +
1087R THR* 3.8 10.4 - - + +
1108R LEU* 4.0 20.6 - - - +
1109R VAL* 1.3 72.0 - - - +
1111R VAL* 1.3 65.7 + - - +
1112R SER* 4.8 0.9 - - - -
1146R PHE* 3.9 30.1 - - + -
1147R PRO* 4.5 9.5 - - + +
1148R GLU* 5.2 4.6 + - + +
1176R TYR* 4.2 18.2 + - - +
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Residues in contact with VAL1111 (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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1012R LYS* 3.2 12.1 - - + +
1013R LYS 3.9 17.7 - - - +
1014R PRO* 3.9 4.5 - - + -
1082R LEU* 4.0 29.6 - - + -
1083R ARG 3.8 30.1 - - - +
1084R SER* 3.7 13.9 - - - +
1086R ASP* 4.2 9.6 - - + -
1087R THR* 3.3 21.7 + - - +
1109R VAL* 4.4 16.4 - - + +
1110R THR* 1.3 77.3 - - - +
1112R SER* 1.3 68.0 + - - +
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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
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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