Contacts of the strand formed by residues 911 - 915 (chain A) in PDB entry 4ZYT
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 MET 911 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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890A VAL* 3.2 30.1 - - + +
892A LEU* 4.2 5.2 - - + -
899A LEU* 3.6 33.4 - - + -
903A PHE* 3.8 25.4 - - + -
904A VAL* 4.1 13.0 - - + +
907A TRP* 3.4 22.1 + - + +
909A GLY 3.7 1.7 + - - +
910A LYS* 1.3 80.3 - - - +
912A LEU* 1.3 69.2 + - - +
945A PHE* 3.4 8.0 - - - -
946A VAL* 2.9 53.4 + - + +
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Residues in contact with LEU 912 (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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889A ILE* 3.9 24.5 - - + -
890A VAL 2.8 9.2 + - - +
891A CYS* 3.5 3.7 - - - -
892A LEU* 2.8 35.3 + - - +
910A LYS 4.5 0.2 - - - -
911A MET* 1.3 83.5 - - - +
913A ASN* 1.3 54.5 + - - +
943A VAL* 4.1 13.7 - - + -
944A HIS 3.5 5.4 - - - +
945A PHE* 4.3 7.6 - - + -
946A VAL* 4.0 2.0 - - - -
956A ILE* 3.9 14.6 - - + -
984A PHE* 4.0 17.9 - - + -
987A ALA 4.0 7.6 - - - +
988A LEU* 4.0 33.4 - - + +
991A VAL* 4.1 20.2 - - + -
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Residues in contact with ASN 913 (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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892A LEU* 3.4 22.2 - - + +
894A GLY 5.6 0.7 + - - -
895A PHE 5.0 0.7 + - - +
912A LEU* 1.3 74.9 - - - +
914A ILE* 1.3 80.8 + - - +
915A HIS* 4.0 4.4 + - - +
942A THR 3.6 1.4 - - - +
943A VAL* 3.2 6.6 - - - +
944A HIS* 2.9 59.9 + - + +
946A VAL* 3.6 18.2 - - + -
951A ASP* 3.8 11.7 + - - -
984A PHE* 4.3 4.7 - - - -
1101A GAR 4.9 3.4 - - - -
1102A 3Y9 3.8 24.0 - - - +
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Residues in contact with ILE 914 (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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820A ASN* 4.1 13.5 - - - +
892A LEU 3.4 8.9 + - - +
893A ALA* 4.2 5.6 - - - -
894A GLY 4.4 1.5 + - - +
913A ASN* 1.3 87.9 + - - +
915A HIS* 1.3 59.9 + - - +
941A CYS* 4.3 2.7 - - + -
942A THR 3.4 8.3 - - - +
943A VAL* 3.5 24.7 - - + -
980A GLU* 3.7 39.7 - - + +
983A ILE* 4.0 15.9 - - + -
984A PHE* 3.4 30.5 - - + -
1101A GAR 3.7 26.2 + - - +
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Residues in contact with HIS 915 (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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913A ASN* 4.0 10.1 - - - +
914A ILE* 1.3 76.4 - - - +
916A PRO* 1.4 63.0 - - + +
917A SER* 3.0 27.2 + - - +
919A LEU* 3.5 28.6 - - + +
922A PHE 2.9 25.6 + - - -
924A GLY 3.2 27.1 - - - -
927A ALA* 3.8 9.7 - - + +
941A CYS* 3.3 3.4 - - - +
942A THR* 2.8 36.5 + - - +
944A HIS* 4.5 0.7 - - - +
951A ASP* 3.2 24.9 + - - -
1101A GAR 3.6 15.8 + - - -
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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