Contacts of the strand formed by residues 1088 - 1096 (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 ALA1088 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038R ARG* 4.4 8.5 - - + -
1039R GLN 3.2 32.1 - - - +
1040R ALA* 3.4 5.2 - - + +
1041R PRO* 4.1 5.8 - - - -
1086R ASP 3.3 9.2 + - - +
1087R THR* 1.3 79.0 - - - +
1089R VAL* 1.3 61.1 + - - +
1090R TYR* 3.9 11.3 - - + +
1107R THR 3.9 0.2 - - - +
1108R LEU* 3.3 5.1 - - - +
1109R VAL* 2.8 37.0 + - - +
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Residues in contact with VAL1089 (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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1037R VAL 3.7 0.3 - - - +
1038R ARG* 3.4 3.1 - - - -
1039R GLN* 3.1 32.5 + - + +
1041R PRO* 6.1 2.0 - - + -
1088R ALA* 1.3 77.7 - - - +
1090R TYR* 1.3 63.0 + - - +
1091R PHE* 3.6 34.0 + - + -
1105R GLN 5.1 0.9 - - - +
1106R GLY* 4.0 4.0 - - - -
1107R THR 3.1 25.6 - - - +
1108R LEU* 3.9 20.2 - - + +
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Residues in contact with TYR1090 (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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1006R GLU* 2.8 9.6 - - - +
1018R VAL* 6.1 1.6 - - + -
1020R VAL* 4.8 5.6 - - + -
1036R TRP* 4.2 15.9 - + + -
1037R VAL 3.6 2.9 - - - -
1038R ARG* 2.7 37.3 + - + -
1048R MET* 3.4 36.1 - - + -
1080R LEU* 4.2 15.0 - - + -
1082R LEU* 3.3 18.2 - - + +
1086R ASP* 2.8 25.3 + - - +
1088R ALA* 3.9 10.1 - - + -
1089R VAL* 1.3 74.3 - - - +
1091R PHE* 1.3 60.2 + - - +
1106R GLY* 3.3 0.7 - - - -
1107R THR* 2.7 42.8 + - - +
1109R VAL* 3.4 36.5 - - + +
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Residues in contact with PHE1091 (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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1038Q GLN* 4.0 5.8 - - - -
1042Q GLN 4.0 9.4 - - - -
1043Q ALA* 3.5 34.5 - - + -
1044Q PRO* 4.6 0.7 - - + -
1006R GLU* 3.7 0.9 - - - -
1035R THR 3.7 0.7 - - - +
1036R TRP* 3.2 9.7 - - - -
1037R VAL* 2.5 46.5 + - - +
1039R GLN* 3.5 27.1 - - + -
1045R LEU* 5.0 5.2 - - + -
1089R VAL* 3.8 28.7 - - + -
1090R TYR* 1.3 74.0 - - - +
1092R CYS* 1.3 58.9 + - - +
1093R ALA* 5.5 0.4 - - - +
1103R TRP* 3.6 28.7 - + + -
1104R GLY 3.8 10.8 - - - -
1105R GLN 3.6 17.0 - - - -
1106R GLY* 3.6 10.5 - - - -
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Residues in contact with CYS1092 (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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1004R LEU* 3.8 6.2 - - - +
1006R GLU* 3.1 12.5 + - - +
1022R CYS* 2.0 50.9 - - - -
1034R PHE* 4.7 12.3 - - - -
1035R THR 3.4 5.8 - - - -
1036R TRP* 3.5 26.5 - - + -
1078R VAL* 4.9 4.5 - - - -
1091R PHE* 1.3 71.7 - - - +
1093R ALA* 1.3 65.3 + - - +
1103R TRP* 3.5 2.1 - - - +
1104R GLY 2.9 26.6 + - - +
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Residues in contact with ALA1093 (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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1004R LEU* 3.8 6.5 - - - -
1034R PHE* 3.1 7.6 - - - +
1035R THR 2.6 42.6 + - - +
1037R VAL* 5.7 0.7 - - + -
1091R PHE 5.5 0.2 - - - +
1092R CYS* 1.3 76.6 - - - +
1094R GLY* 1.3 56.4 + - - +
1100R LEU* 3.7 35.7 - - + -
1102R HIS 3.0 16.2 - - - +
1103R TRP* 3.8 16.4 - - + -
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Residues in contact with GLY1094 (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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1004R LEU* 3.8 4.3 - - - +
1032R TYR* 4.7 2.2 - - - -
1033R SER 3.2 13.9 - - - -
1034R PHE* 4.1 12.1 - - - -
1093R ALA* 1.3 76.1 - - - +
1095R VAL* 1.3 62.6 + - - -
1100R LEU* 4.9 4.3 - - - -
1101R LYS 3.3 6.6 + - - -
1102R HIS* 2.7 42.3 + - - +
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Residues in contact with VAL1095 (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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1032R TYR* 3.3 11.0 - - - -
1033R SER* 3.3 29.2 + - - +
1094R GLY* 1.3 76.1 - - - +
1096R TYR* 1.3 75.5 + - + +
1097R GLU* 3.4 19.6 + - - +
1100R PHE* 3.4 67.3 - - + +
1101R LYS* 4.3 9.9 - - + +
1102R HIS* 4.6 4.3 - - - -
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Residues in contact with TYR1096 (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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1027R ASP* 4.4 7.6 - - - -
1031R ARG* 3.2 50.4 + - + -
1032R TYR* 3.3 34.6 - + + +
1095R VAL* 1.3 79.9 - - + +
1097R GLU* 1.3 58.6 + - - +
1098R GLY* 3.3 42.4 - - - -
1099R GLU* 3.6 4.7 + - - +
1100R ASN* 3.4 19.2 + - - +
1102R HIS* 5.1 2.5 + - - +
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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