Contacts of the strand formed by residues 936 - 941 (chain B) in PDB entry 5D6Y
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 SER 936 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931B ASN* 3.6 2.6 - - - -
932B PHE* 2.9 25.4 + - - +
934B ASP* 2.7 30.9 + - - -
935B GLY* 1.3 81.0 - - - +
937B PHE* 1.3 66.4 + - - +
23b M3L 3.5 27.5 - - - +
24b ALA 3.3 19.7 - - - -
25b ALA* 4.4 2.7 - - - +
26b ARG* 4.1 2.0 + - - -
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Residues in contact with PHE 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929B GLU* 3.8 21.1 - - - -
930B VAL 3.3 6.5 - - - +
931B ASN* 3.3 21.3 - - - +
932B PHE* 4.3 3.1 - - - -
936B SER* 1.3 77.3 - - - +
938B SER* 1.3 68.1 + - - +
939B ASP* 3.7 26.0 - - - -
23b M3L 3.3 7.3 - - - +
24b ALA* 2.9 61.2 + - + +
25b ALA 3.8 14.6 - - - -
26b ARG* 4.0 23.8 - - + -
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Residues in contact with SER 938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B TYR 3.7 1.3 - - - +
929B GLU* 3.1 3.6 - - - +
930B VAL* 2.9 32.5 + - - +
932B PHE* 3.9 19.8 - - - -
937B PHE* 1.3 76.6 - - - +
939B ASP* 1.3 60.9 + - - +
940B ASN* 3.2 11.4 + - - -
941B LEU* 3.4 20.7 - - - +
967B TRP* 4.0 7.4 - - - -
21b ALA* 3.9 2.8 - - - +
22b THR 3.0 24.0 + - - -
23b M3L 4.4 0.2 - - - -
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Residues in contact with ASP 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B PHE* 3.6 12.1 - - - +
928B TYR 3.3 13.3 - - - +
929B GLU* 3.7 28.8 - - + +
937B PHE* 3.7 19.0 - - + -
938B SER* 1.3 73.5 + - - +
940B ASN* 1.3 72.8 + - - +
981B HIS* 4.1 12.7 - - + +
983B ILE* 5.0 3.6 - - - +
22b THR 4.6 0.4 + - - +
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Residues in contact with ASN 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B PHE* 3.6 27.3 - - + -
938B SER* 3.2 5.6 + - - -
939B ASP* 1.3 92.4 + - - +
941B LEU* 1.3 61.3 + - - +
942B TYR* 3.9 3.8 + - - -
999B LYS* 4.3 14.9 - - - +
19b GLN 5.1 1.6 - - - +
20b LEU 4.7 5.0 + - - -
21b ALA* 3.2 14.7 + - - +
22b THR* 2.9 46.0 + - - +
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Residues in contact with LEU 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B PHE* 3.4 9.3 - - - -
928B TYR* 2.7 44.9 + - + +
930B VAL* 3.3 45.8 - - + +
938B SER* 3.4 11.2 - - - +
940B ASN* 1.3 78.5 - - - +
942B TYR* 1.3 65.7 + - - +
945B ASP* 4.2 12.8 - - + +
946B ILE* 5.1 4.0 - - + -
965B VAL* 3.9 18.6 - - + -
967B TRP* 3.5 34.1 - - + -
21b ALA* 3.7 7.4 - - + -
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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