Contacts of the strand formed by residues 1085 - 1090 (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 VAL1085 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1036Q TYR 4.0 0.2 - - - +
1037Q GLN* 3.6 2.4 - - - -
1038Q GLN* 2.8 40.0 + - - +
1040Q PRO* 5.9 2.0 - - + +
1084Q ALA* 1.3 75.5 - - - +
1086Q TYR* 1.3 70.5 + - - +
1087Q TYR* 3.5 37.4 + - + +
1100Q GLN 5.6 0.2 - - - +
1101Q GLY* 4.6 1.3 - - - -
1102Q THR 3.2 13.2 - - - +
1103Q ARG* 3.5 30.3 - - + -
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Residues in contact with TYR1086 (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* 2.7 25.1 + - - +
1021Q LEU* 3.7 28.5 - - + -
1035Q TRP* 4.7 6.7 - + + -
1036Q TYR 3.2 8.1 - - - +
1037Q GLN* 3.0 30.4 + - + -
1047Q LEU* 3.6 17.5 - - + -
1062Q PHE* 3.5 28.7 - + - -
1073Q LEU* 3.9 9.6 - - + -
1075Q ILE* 3.9 8.4 - - + +
1082Q ASP* 2.4 38.2 + - - +
1084Q ALA 3.8 18.8 - - - -
1085Q VAL* 1.3 77.4 - - - +
1087Q TYR* 1.3 57.8 + - - +
1101Q GLY* 3.3 2.9 - - - -
1102Q THR 2.8 25.2 + - - -
1104Q LEU* 3.9 13.0 - - + -
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Residues in contact with TYR1087 (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* 3.6 4.5 - - - +
1035Q TRP* 3.3 5.6 - - - -
1036Q TYR* 2.7 45.7 + - + -
1038Q GLN* 3.2 31.8 + - + -
1085Q VAL* 3.5 25.1 - - + +
1086Q TYR* 1.3 76.9 - - - +
1088Q CYS* 1.3 64.1 + - - +
1098Q PHE* 4.7 3.8 - - + -
1099Q GLY 3.6 16.4 - - - -
1100Q GLN 3.4 21.4 + - - -
1101Q GLY* 3.6 9.9 - - - -
1039R GLN* 3.5 9.6 + - - -
1043R GLN 3.6 4.7 + - - -
1044R GLY* 3.5 28.3 - - - -
1045R LEU* 3.8 34.5 - - + -
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Residues in contact with CYS1088 (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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1004Q MET* 4.4 5.4 - - - -
1005Q THR 5.3 0.2 - - - -
1006Q GLN* 3.4 22.2 + - - -
1023Q CYS* 2.1 52.5 - - + -
1033Q LEU* 3.8 4.7 - - + -
1034Q ALA 3.1 10.8 - - - +
1035Q TRP* 4.0 13.0 - - + -
1036Q TYR* 5.0 0.2 - - - -
1087Q TYR* 1.3 74.3 - - - +
1089Q GLN* 1.3 60.2 + - - +
1098Q PHE* 3.1 5.8 - - - +
1099Q GLY* 2.7 34.9 + - - -
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Residues in contact with GLN1089 (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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1004Q MET* 5.0 1.1 - - - -
1033Q LEU* 3.2 10.3 - - - +
1034Q ALA* 2.9 32.8 + - - +
1036Q TYR* 2.8 33.8 + - + -
1088Q CYS* 1.3 75.5 - - - +
1090Q GLN* 1.3 66.8 + - - +
1091Q TYR* 3.7 19.9 + - - +
1096Q TYR* 3.8 12.1 - - + +
1097Q THR 3.3 16.4 - - - +
1098Q PHE* 3.3 34.9 - - + -
1047R TRP* 4.5 5.9 - - - -
1100R LEU* 3.2 27.6 - - - +
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Residues in contact with GLN1090 (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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1002Q ILE* 3.9 18.9 - - + +
1004Q MET* 3.8 19.5 - - + +
1029Q VAL* 3.2 37.0 - - + -
1032Q ASP 3.4 4.7 - - - -
1033Q LEU* 4.5 0.4 - - - +
1089Q GLN* 1.3 76.1 - - - +
1091Q TYR* 1.3 61.4 + - - +
1092Q ASN* 3.9 3.9 + - + +
1093Q ASN* 3.3 33.3 + - - +
1095Q ARG 4.2 1.2 - - - -
1096Q TYR* 3.3 20.1 - - - +
1097Q THR* 2.4 50.5 + - - +
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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