Contacts of the strand formed by residues 1006 - 1010 (chain A) in PDB entry 2YIC
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 VAL1006 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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970A MET* 4.4 4.5 - - + -
971A VAL 2.8 21.2 + - - +
972A LEU* 3.9 21.8 - - + -
973A TRP* 2.7 32.7 + - - +
1005A VAL* 1.3 73.2 - - - +
1007A LEU* 1.3 62.9 + - - +
1008A LEU* 3.7 26.7 - - + -
1052A LEU* 4.6 1.1 - - + -
1055A HIS* 3.4 38.8 - - + +
1064A LEU* 3.3 17.0 - - + +
1066A VAL* 4.0 11.4 - - + -
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Residues in contact with LEU1007 (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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956A VAL* 4.2 13.9 - - + -
973A TRP* 3.4 26.7 - - + +
981A VAL* 4.6 9.2 - - + -
988A ILE* 4.2 18.6 - - + -
992A ILE* 3.9 24.2 - - + -
1005A VAL* 4.4 12.1 - - + -
1006A VAL* 1.3 79.1 - - - +
1008A LEU* 1.3 57.8 + - - +
1009A LEU* 3.9 15.3 + - + +
1028A PHE* 4.4 7.6 - - + -
1064A LEU 2.9 7.9 + - - +
1065A ILE* 3.6 27.9 - - + -
1066A VAL* 2.9 32.6 + - - +
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Residues in contact with LEU1008 (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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882A GLU* 3.7 11.4 - - - +
898A LEU* 4.4 12.3 - - + -
911A ARG* 4.5 4.7 - - - +
972A LEU* 4.1 23.1 - - + -
973A TRP 2.9 15.0 + - - +
974A GLU* 3.6 18.7 - - + +
975A ALA 3.0 25.5 + - - -
1006A VAL* 3.7 25.1 - - + -
1007A LEU* 1.3 70.3 - - - +
1009A LEU* 1.3 61.3 + - - +
1010A PRO* 3.6 4.7 - - - +
1048A TYR* 3.3 28.7 - - + +
1052A LEU* 4.9 0.2 - - + -
1066A VAL* 3.6 20.0 - - + -
1068A THR* 4.1 11.7 - - + +
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Residues in contact with LEU1009 (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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973A TRP* 4.0 6.3 - - + -
975A ALA* 3.8 17.5 - - + -
978A GLY* 3.8 11.0 - - - -
981A VAL* 3.8 25.1 - - + -
1007A LEU* 4.2 11.9 - - + +
1008A LEU* 1.3 82.2 - - - +
1010A PRO* 1.4 69.2 - - - +
1011A HIS* 3.2 3.8 + - - +
1023A GLY 4.2 3.1 - - - +
1028A PHE* 3.6 35.9 - - + -
1065A ILE* 3.7 17.5 - - + -
1066A VAL 2.7 15.3 + - - +
1067A PHE* 3.3 21.9 - - + -
1068A THR* 3.1 18.7 + - - -
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Residues in contact with PRO1010 (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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908A PHE* 4.0 11.9 - - + -
974A GLU* 4.8 9.6 - - + +
975A ALA 3.2 21.5 - - - +
976A GLN 3.5 22.0 - - - +
977A PHE* 3.8 3.8 - - - +
978A GLY* 2.8 36.2 + - - +
979A ASP* 4.4 4.5 - - - +
1008A LEU 3.6 4.9 - - - +
1009A LEU* 1.4 78.8 - - - +
1011A HIS* 1.3 58.1 - - - +
1023A GLY 4.6 0.9 + - - -
1068A THR* 3.2 19.5 - - - +
1069A PRO 4.5 2.2 - - - +
1070A LYS* 3.8 27.2 + - + +
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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