Contacts of the strand formed by residues 960 - 965 (chain B) in PDB entry 4DQL
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 THR 960 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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930B GLU* 5.8 2.1 - - - +
931B ALA 2.9 9.5 + - - -
932B HIS* 3.4 24.7 + - + +
933B LEU 3.0 24.4 + - - -
954B GLN* 3.9 8.1 - - - +
959B ILE* 1.3 76.9 + - - +
961B LEU* 1.3 61.8 + - - +
962B HIS* 3.4 27.1 - - + +
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Residues in contact with LEU 961 (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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933B LEU* 3.6 34.5 - - + +
935B PHE* 4.8 7.4 - - + -
944B TYR* 3.4 26.0 - - - +
950B LEU* 3.7 33.9 - - + +
951B GLU* 4.0 12.8 - - + +
954B GLN* 3.0 28.7 + - - +
959B ILE* 3.9 13.9 - - + -
960B THR* 1.3 75.0 - - - +
962B HIS* 1.3 66.4 + - - +
963B THR* 4.2 6.0 + - + -
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Residues in contact with HIS 962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B HIS* 2.8 33.1 + + + -
933B LEU 2.8 13.9 + - - +
934B TYR* 3.3 40.2 + + + +
935B PHE 2.9 26.6 + - - +
960B THR* 3.4 28.5 - - + +
961B LEU* 1.3 75.1 + - - +
963B THR* 1.3 63.8 + - - +
964B ALA* 5.4 0.2 - - - +
976B VAL* 5.2 0.9 - - - +
979B VAL* 4.2 9.4 - - + +
983B ASP* 3.5 21.9 + - - -
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Residues in contact with THR 963 (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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935B PHE* 3.2 13.2 - - + +
944B TYR* 3.4 34.1 - - + +
961B LEU* 4.2 8.7 - - + -
962B HIS* 1.3 77.8 - - - +
964B ALA* 1.3 62.7 + - - +
965B PHE* 3.6 32.4 - - + -
974B THR* 5.4 0.3 - - - +
979B VAL* 4.1 11.1 - - - +
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Residues in contact with ALA 964 (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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935B PHE 2.9 11.6 + - - +
936B GLY* 3.1 3.3 - - - -
937B CYS 3.1 25.1 + - - +
962B HIS 5.4 0.2 - - - +
963B THR* 1.3 76.1 - - - +
965B PHE* 1.3 63.7 + - - +
974B THR* 3.5 14.1 - - - +
975B TYR 3.5 35.0 - - - +
976B VAL* 3.6 11.0 - - + +
979B VAL* 4.1 8.5 - - + -
1102B NAP 4.7 1.0 + - - -
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Residues in contact with PHE 965 (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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935B PHE* 5.3 1.3 - + - -
937B CYS* 3.2 35.2 - - - -
938B ARG 3.9 3.4 - - - +
939B SER 4.1 0.2 - - - -
940B PRO* 3.5 42.0 - - + -
944B TYR* 4.0 17.3 - + - -
963B THR* 3.6 34.8 - - + -
964B ALA* 1.3 73.7 - - - +
966B SER* 1.3 61.6 + - - +
967B ARG 3.7 0.9 - - - -
968B MET* 3.8 40.7 + - + +
971B GLN* 5.9 0.7 - - - +
972B PRO 4.0 4.7 - - - +
974B THR* 3.2 23.1 + - - -
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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