Contacts of the strand formed by residues 97 - 104 (chain A) in PDB entry 5J9S
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 LYS 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLU* 2.6 32.1 + - + +
87A VAL 3.2 15.5 - - - +
88A HIS* 3.7 32.0 - - + +
89A PHE* 3.7 10.3 - - - -
94A GLU* 6.1 0.2 - - - +
95A PRO* 3.3 12.4 - - - +
96A ARG* 1.3 84.9 - - + +
98A VAL* 1.3 63.9 + - - +
99A CYS* 4.2 15.0 - - - -
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Residues in contact with VAL 98 (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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11A LEU* 4.7 0.2 - - + -
85A ILE 3.8 0.9 - - - +
86A GLU* 3.5 1.6 - - - -
87A VAL* 2.9 44.0 + - + +
89A PHE* 3.5 24.7 - - + -
97A LYS* 1.3 75.4 - - - +
99A CYS* 1.3 71.9 + - - +
100A PHE* 3.6 35.2 - - + -
122A LEU* 4.2 17.5 - - + -
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Residues in contact with CYS 99 (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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85A ILE 3.4 6.5 - - - +
86A GLU* 3.8 28.7 - - + -
97A LYS* 4.2 16.6 - - - -
98A VAL* 1.3 82.3 - - - +
100A PHE* 1.3 69.1 + - - +
101A THR* 6.4 0.4 - - + -
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Residues in contact with PHE 100 (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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11A LEU* 4.2 9.6 - - + -
13A LEU* 3.6 31.9 - - + -
84A PRO* 3.4 5.0 - - - +
85A ILE* 2.7 45.5 + - + +
87A VAL* 3.5 29.8 - - + -
98A VAL* 3.6 30.3 - - + -
99A CYS* 1.3 78.7 - - - +
101A THR* 1.3 65.5 + - - +
102A TYR 4.1 0.2 - - - -
118A ARG* 4.6 5.8 - - - +
120A GLU* 3.7 38.4 - - + -
122A LEU* 4.2 13.7 - - + -
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Residues in contact with THR 101 (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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82A ILE* 4.1 19.3 - - + -
83A MET 3.7 3.8 - - - -
84A PRO* 4.4 11.0 - - + -
99A CYS* 5.9 0.4 - - + -
100A PHE* 1.3 79.8 - - - +
102A TYR* 1.3 59.8 + - - +
103A ASP 4.2 0.5 + - - -
118A ARG* 3.1 18.6 + - - +
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Residues in contact with TYR 102 (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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13A LEU* 4.0 15.0 - - + -
14A GLY* 3.3 23.1 - - - -
15A HIS* 2.6 54.6 + + + -
34A VAL* 4.3 11.2 - - + -
82A ILE* 3.4 4.3 - - - -
83A MET* 2.6 49.0 + - + +
85A ILE* 3.7 18.8 - - + -
100A PHE 4.1 0.2 - - - -
101A THR* 1.3 73.0 - - - +
103A ASP* 1.3 73.6 + - - +
104A LEU* 3.4 9.7 + - + -
116A HIS* 3.2 18.2 + + - -
118A ARG* 3.6 35.0 - - + +
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Residues in contact with ASP 103 (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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15A HIS* 3.8 0.2 - - - -
82A ILE* 3.7 15.7 - - + +
101A THR 4.2 1.0 + - - -
102A TYR* 1.3 86.4 - - - +
104A LEU* 1.3 58.2 + - - +
105A PHE* 3.2 33.7 + - + +
116A HIS* 5.4 0.5 + - - -
118A ARG* 4.9 1.6 - - - +
26B ARG* 2.6 43.9 + - - -
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Residues in contact with LEU 104 (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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15A HIS* 3.9 18.4 - - + -
32A TRP* 3.4 61.0 - - + +
34A VAL* 3.8 16.2 - - + -
79A ALA 5.2 0.4 - - - +
80A GLY* 3.1 8.8 - - - -
81A PHE* 2.9 47.7 + - + +
83A MET* 3.5 27.6 - - + -
102A TYR* 3.4 10.0 + - + +
103A ASP* 1.3 69.4 - - - +
105A PHE* 1.3 57.0 + - - +
106A LEU* 4.1 8.7 - - + -
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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