Contacts of the strand formed by residues 1070 - 1075 (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 GLU1070 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023Q CYS 3.6 3.4 - - - -
1024Q ARG* 3.8 34.0 + - + +
1066Q GLY* 3.5 3.6 - - - -
1067Q SER 2.9 26.7 + - - +
1068Q GLY 3.6 0.4 - - - -
1069Q ALA* 1.3 87.4 - - - +
1071Q PHE* 1.3 63.2 + - - +
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Residues in contact with PHE1071 (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* 4.7 7.4 - - + -
1022Q SER* 3.4 4.2 - - - -
1023Q CYS* 2.8 46.7 + - + +
1025Q ALA* 5.0 0.2 - - + -
1029Q VAL* 4.4 11.4 - - + -
1030Q SER 3.6 13.9 - - - -
1033Q LEU* 3.6 51.8 - - + -
1035Q TRP* 4.4 2.9 - - + +
1051Q ALA* 4.2 9.2 - - + -
1065Q SER 3.5 7.0 - - - +
1066Q GLY* 3.6 16.8 - - - -
1067Q SER* 3.4 19.1 - - - -
1068Q GLY 3.3 26.9 - - - -
1069Q ALA* 3.7 4.0 - - - -
1070Q GLU* 1.3 81.3 - - - +
1072Q THR* 1.3 68.7 + - - +
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Residues in contact with THR1072 (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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1020Q THR* 4.5 14.4 - - + -
1021Q LEU 3.4 12.8 + - - +
1022Q SER* 4.2 7.6 - - - -
1035Q TRP* 3.9 5.9 + - - -
1064Q GLY* 3.3 2.9 - - - -
1065Q SER* 2.8 49.9 + - - +
1071Q PHE* 1.3 80.0 + - - +
1073Q LEU* 1.3 62.4 + - - +
1074Q THR* 3.9 21.8 + - + +
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Residues in contact with LEU1073 (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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1021Q LEU* 2.9 43.2 + - + +
1035Q TRP* 3.2 45.9 - - + +
1047Q LEU* 4.5 3.1 - - + -
1048Q ILE* 4.0 17.9 - - + -
1062Q PHE* 4.6 7.9 - - + -
1063Q SER 3.2 26.9 - - - +
1064Q GLY* 4.4 0.4 - - - -
1072Q THR* 1.3 72.7 - - - +
1074Q THR* 1.3 63.6 + - - +
1075Q ILE* 4.4 8.7 - - + -
1086Q TYR* 3.9 32.3 - - + -
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Residues in contact with THR1074 (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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1018Q ARG* 4.0 19.9 + - - +
1019Q ALA 3.4 9.5 + - - -
1020Q THR* 3.9 18.2 - - - +
1061Q ARG 3.5 0.7 - - - +
1062Q PHE* 4.0 0.2 - - - -
1063Q SER* 2.9 61.1 + - - +
1064Q GLY* 4.8 2.7 - - - +
1065Q SER* 5.7 2.7 - - - +
1072Q THR* 4.3 9.9 - - + +
1073Q LEU* 1.3 75.3 - - - +
1075Q ILE* 1.3 62.8 + - - +
1076Q SER 4.1 0.4 + - - -
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Residues in contact with ILE1075 (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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1018Q ARG* 3.4 5.8 - - - +
1019Q ALA* 3.0 34.1 + - + +
1021Q LEU* 4.6 3.6 - - + -
1061Q ARG* 3.2 12.3 - - + +
1062Q PHE* 3.5 36.8 - - + -
1073Q LEU* 4.4 11.2 - - + +
1074Q THR* 1.3 75.1 + - - +
1076Q SER* 1.3 63.4 + - - +
1077Q SER 4.0 5.2 - - - +
1078Q LEU* 4.0 32.8 - - + +
1082Q ASP* 4.3 7.9 - - + +
1086Q TYR* 3.9 16.4 - - + +
1104Q LEU* 4.0 22.4 - - + -
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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