Contacts of the strand formed by residues 1069 - 1073 (chain B) in PDB entry 5JHN
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 GLY1069 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953B ILE* 4.1 6.3 - - - -
956B ASN* 3.0 14.3 + - - +
957B CYS 3.0 23.8 + - - -
1068B VAL* 1.3 79.1 - - - +
1070B GLU* 1.3 62.9 + - - -
1099B ILE* 3.3 14.5 - - - +
1100B ASP 3.8 1.8 - - - -
1101B ALA* 4.4 0.2 - - - -
1104B TYR 3.2 17.3 - - - -
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Residues in contact with GLU1070 (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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957B CYS* 3.5 18.6 - - - +
959B THR* 2.6 46.8 + - + +
1069B GLY* 1.3 71.1 - - - -
1071B LEU* 1.3 67.2 + - - +
1072B ILE* 3.5 8.2 + - + +
1080B ARG* 2.8 42.6 + - - -
1099B ILE* 3.4 2.9 - - - -
1100B ASP* 2.8 42.9 + - + +
1103B TYR* 4.2 8.3 - - - +
1104B TYR* 3.7 18.9 + - + -
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Residues in contact with LEU1071 (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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956B ASN* 4.1 31.2 - - + +
957B CYS 2.8 21.7 + - - +
958B GLU* 4.7 8.5 - - + -
959B THR* 4.4 9.5 + - - -
960B SER* 5.1 1.0 + - - -
962B MET* 4.2 17.5 - - + +
964B ILE* 3.9 27.6 - - + -
1070B GLU* 1.3 75.0 - - - +
1072B ILE* 1.3 65.3 + - - +
1089B LEU* 4.2 8.7 - - + -
1098B CYS 3.5 2.7 - - - +
1099B ILE* 3.9 24.7 - - + -
1133B PHE* 4.0 33.7 - - + -
1134B PRO 5.9 0.2 - - - +
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Residues in contact with ILE1072 (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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959B THR* 4.6 2.0 - - - +
960B SER* 5.8 0.9 - - - -
962B MET* 4.7 4.5 - - - -
1070B GLU* 3.7 19.1 - - + +
1071B LEU* 1.3 81.9 - - - +
1073B SER* 1.3 66.5 + - - +
1076B GLU* 4.1 9.0 - - + -
1077B ALA* 3.6 31.0 - - + +
1080B ARG* 3.6 33.2 - - + +
1086B LEU* 4.0 6.1 - - + -
1097B TYR* 3.4 10.0 - - - +
1098B CYS* 2.8 47.1 + - + +
1100B ASP* 3.8 20.9 - - + -
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Residues in contact with SER1073 (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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962B MET* 4.8 7.4 - - - +
1072B ILE* 1.3 77.9 - - - +
1074B ASP* 1.3 59.3 + - - +
1075B ALA* 3.6 9.0 + - - +
1076B GLU* 3.1 24.2 + - - +
1077B ALA* 2.9 28.5 + - - +
1097B TYR* 3.8 21.9 - - - -
1098B CYS 4.8 0.4 - - - -
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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