Contacts of the strand formed by residues 88 - 93 (chain A) in PDB entry 1JK8
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 GLU 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A VAL* 4.5 7.2 - - + +
87A PRO* 1.3 75.4 - - - +
89A VAL* 1.3 61.7 + - - +
90A THR* 5.0 3.3 + - - +
108A LEU 3.4 2.1 - - - +
109A VAL* 3.5 1.0 - - - -
110A ASP* 2.7 53.7 + - + +
111A ASN* 4.7 9.2 - - + +
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Residues in contact with VAL 89 (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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87A PRO* 4.0 4.2 + - + +
88A GLU* 1.3 75.5 - - - +
90A THR* 1.3 69.7 + - - +
107A CYS* 3.7 27.8 - - - -
108A LEU 3.3 4.5 - - - +
109A VAL* 4.6 4.0 - - + -
163A CYS* 4.5 1.3 - - + +
165A VAL* 3.5 32.8 - - + -
174A LEU* 3.6 29.2 - - + +
176A LYS* 3.4 48.4 + - + +
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 5.0 3.5 - - - +
89A VAL* 1.3 79.5 + - - +
91A VAL* 1.3 69.4 + - - +
92A PHE* 4.2 16.4 - - + -
106A ILE 3.7 1.2 - - - +
107A CYS* 3.5 1.4 - - - -
108A LEU* 2.8 52.7 + - + +
176A LYS* 5.1 1.8 - - - +
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Residues in contact with VAL 91 (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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90A THR* 1.3 82.8 - - - +
92A PHE* 1.3 66.9 + - - +
105A LEU* 4.1 15.0 - - + -
106A ILE 3.3 7.0 - - - +
107A CYS* 3.9 8.3 - - + -
121A TRP* 4.6 4.0 - - + -
163A CYS* 3.6 31.2 - - + -
176A LYS* 3.8 25.6 - - + +
177A HIS 4.9 2.7 - - - +
178A TRP* 3.6 41.2 - - + -
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Residues in contact with PHE 92 (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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90A THR* 4.2 20.9 - - + -
91A VAL* 1.3 81.9 - - - +
93A SER* 1.3 70.3 + - - +
105A LEU* 3.9 5.4 - - - -
106A ILE* 2.7 74.8 + - + +
108A LEU* 4.5 16.2 - - + -
148A ILE* 6.1 0.2 - - + -
178A TRP* 4.3 6.3 - - - +
148B ILE* 3.7 29.4 - - + -
149B ARG 4.5 8.3 - - - -
150B ASN* 3.4 23.6 - - - -
156B GLN* 3.9 7.9 - - - +
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Residues in contact with SER 93 (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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92A PHE* 1.3 84.3 - - - +
94A LYS* 1.3 61.6 + - - +
95A SER 2.4 31.7 + - - -
97A VAL* 3.5 18.1 - - - +
103A ASN* 3.4 10.2 + - - -
104A THR 3.9 5.2 - - - -
105A LEU* 4.1 6.4 - - - +
153A PHE* 5.4 0.4 - - - -
178A TRP* 4.1 13.1 - - - +
156B GLN* 3.3 21.1 - - - +
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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