Contacts of the strand formed by residues 1033 - 1038 (chain Q) 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 LEU1033 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004Q MET* 3.9 9.6 - - + -
1023Q CYS* 3.8 25.4 - - - -
1029Q VAL* 4.9 1.8 - - + -
1031Q SER 2.8 8.3 + - - +
1032Q ASP* 1.3 75.2 - - - +
1034Q ALA* 1.3 62.5 + - - +
1035Q TRP* 3.5 32.9 - - + +
1048Q ILE 4.7 0.2 - - - -
1049Q TYR* 3.6 0.9 - - - -
1050Q GLY 3.5 4.0 + - - -
1051Q ALA* 3.1 28.9 + - - -
1071Q PHE* 3.6 47.3 - - + -
1088Q CYS* 3.8 8.5 - - + -
1089Q GLN 3.2 20.9 - - - +
1091Q TYR* 3.7 3.6 - - - -
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Residues in contact with ALA1034 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033Q LEU* 1.3 75.3 - - - +
1035Q TRP* 1.3 64.8 + - - +
1036Q TYR* 3.7 28.9 - - + +
1046Q LEU* 5.1 0.7 - - + -
1048Q ILE 3.2 13.5 - - - +
1049Q TYR* 4.1 1.8 - - + -
1088Q CYS* 3.1 9.4 - - - +
1089Q GLN* 2.9 32.7 + - - +
1091Q TYR* 4.0 5.6 - - + -
1100R PHE* 4.0 18.8 - - - -
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Residues in contact with TRP1035 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006Q GLN* 3.7 21.8 - - - -
1021Q LEU* 3.8 20.4 - - + -
1022Q SER 4.0 4.9 - - - -
1023Q CYS* 3.5 31.2 - - + -
1033Q LEU* 3.5 23.2 - - + +
1034Q ALA* 1.3 72.7 - - - +
1036Q TYR* 1.3 67.7 + - - +
1046Q LEU* 3.9 1.0 - - - +
1047Q LEU* 2.9 31.3 + - + -
1048Q ILE* 2.8 38.7 + - + +
1051Q ALA 4.9 3.9 + - - -
1064Q GLY* 5.1 0.4 - - - -
1065Q SER 5.3 0.4 + - - -
1071Q PHE* 4.4 3.4 - - + +
1072Q THR* 3.9 15.8 + - - -
1073Q LEU* 3.2 54.8 - - + +
1086Q TYR* 4.7 7.6 - - + -
1087Q TYR 3.3 17.7 - - - -
1088Q CYS* 4.0 5.4 - - + -
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Residues in contact with TYR1036 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034Q ALA* 3.7 18.4 - - + -
1035Q TRP* 1.3 75.8 - - - +
1037Q GLN* 1.3 60.5 + - - +
1044Q PRO* 4.3 12.6 - - + -
1045Q ARG 3.2 17.9 - - - +
1046Q LEU* 4.0 10.3 - - + -
1047Q LEU* 4.0 4.7 - - - -
1086Q TYR* 3.2 9.5 - - - +
1087Q TYR* 2.7 49.4 + - + +
1089Q GLN* 2.8 36.1 + - + -
1098Q PHE* 3.9 17.5 - + - -
1045R LEU* 5.0 1.8 - - + -
1100R LEU* 2.7 54.9 + - + +
1103R TRP* 3.8 22.0 - + - -
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Residues in contact with GLN1037 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036Q TYR* 1.3 73.9 - - - +
1038Q GLN* 1.3 64.2 + - - +
1039Q LYS* 3.1 25.9 + - - +
1043Q ALA 4.4 0.5 - - - +
1044Q PRO* 3.3 3.3 - - - +
1045Q ARG* 2.9 51.9 + - + +
1047Q LEU* 3.9 16.8 - - + +
1062Q PHE* 3.7 16.6 - - - -
1081Q GLU 3.5 17.3 + - - -
1082Q ASP* 4.0 2.2 + - - +
1084Q ALA* 4.2 9.4 - - + -
1085Q VAL 3.6 3.1 - - - -
1086Q TYR* 3.0 41.7 + - + -
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Residues in contact with GLN1038 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037Q GLN* 1.3 79.0 - - - +
1039Q LYS* 1.3 72.3 + - - +
1040Q PRO* 4.1 1.4 - - + +
1042Q GLN 3.0 21.7 + - - +
1043Q ALA 4.4 1.8 - - - -
1044Q PRO* 3.6 33.6 - - + +
1084Q ALA* 4.0 2.9 - - - -
1085Q VAL* 2.8 38.1 + - - +
1087Q TYR* 3.2 22.9 + - + -
1039R GLN* 3.0 40.0 + - - +
1045R LEU* 4.0 1.2 - - - +
1091R PHE* 4.0 4.6 - - - -
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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