Contacts of the strand formed by residues 1016 - 1021 (chain A) in PDB entry 1YW2
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 THR1016 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012A GLU* 3.0 4.2 - - - -
1013A LEU 2.7 42.0 + - - -
1014A ASN 3.2 3.3 + - - -
1015A LYS* 1.3 81.5 + - - +
1017A ILE* 1.3 66.4 + - - +
1018A TRP* 3.7 12.0 - - - +
1037A SER* 4.5 18.6 + - - +
1054A LYS* 4.7 12.3 - - + +
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Residues in contact with ILE1017 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010A ARG* 4.3 16.2 - - + -
1011A GLN 3.3 10.1 - - - +
1012A GLU* 3.6 27.4 - - + +
1015A LYS 4.8 1.8 - - - +
1016A THR* 1.3 76.9 - - - +
1018A TRP* 1.3 70.6 + - - +
1019A GLU* 3.8 10.5 - - + +
1054A LYS* 3.0 33.8 + - - +
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Residues in contact with TRP1018 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A TYR 3.4 3.2 - - - +
1010A ARG* 3.1 25.1 - - - -
1011A GLN* 2.9 23.6 + - + +
1013A LEU* 3.8 28.0 + - + +
1016A THR* 3.7 25.9 - - - +
1017A ILE* 1.3 77.9 - - - +
1019A GLU* 1.3 62.4 + - - +
1020A VAL* 4.0 15.5 - - + -
1027A LEU* 4.3 9.4 - - + -
1037A SER* 3.2 35.1 - - - -
1038A VAL 4.5 0.2 - - - -
1039A CYS* 3.5 25.3 - - + -
1052A VAL* 3.1 46.9 - - + -
1054A LYS* 3.5 17.3 - - + -
1103A TYR* 3.5 20.9 - + - -
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Residues in contact with GLU1019 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008A PHE* 3.4 14.4 - - - -
1009A TYR 3.9 4.9 - - - -
1010A ARG* 3.7 38.9 + - - +
1017A ILE* 3.8 11.4 - - + +
1018A TRP* 1.3 73.9 - - - +
1020A VAL* 1.3 59.3 + - - +
1054A LYS* 3.3 8.7 + - - -
1090A PHE* 3.6 2.9 - - - -
1092A PRO* 3.0 33.4 - - + +
1101A ASP* 2.8 24.5 - - - +
1103A TYR* 2.7 44.0 + - - -
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Residues in contact with VAL1020 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008A PHE* 3.3 7.0 - - - +
1009A TYR* 3.3 50.9 + - + +
1011A GLN* 5.7 0.2 - - - +
1018A TRP* 4.3 15.7 - - + -
1019A GLU* 1.3 77.7 - - - +
1021A PRO* 1.3 82.2 - - + +
1024A TYR* 4.6 9.0 - - + +
1027A LEU* 4.7 15.3 - - + -
1052A VAL* 4.5 4.9 - - + -
1090A PHE* 3.3 24.0 - - + -
1103A TYR* 3.9 15.7 - - + -
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Residues in contact with PRO1021 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A PRO* 4.0 23.6 - - + -
1007A THR 3.5 8.5 - - - +
1008A PHE* 3.6 16.5 - - + -
1020A VAL* 1.3 97.5 - - + +
1022A GLU* 1.3 64.9 + - - +
1023A ARG* 3.0 19.2 + - + -
1024A TYR* 3.4 22.0 + - + +
1088A ASP* 5.3 1.8 - - - +
1090A PHE* 3.3 37.0 - - + -
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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