Contacts of the strand formed by residues 97 - 102 (chain E) in PDB entry 3TJK
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 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93E VAL* 3.3 4.0 - - - -
94E ILE* 2.8 39.5 + - - +
95E ASP 4.0 7.0 - - - +
96E GLY* 1.3 83.3 - - - +
98E PHE* 1.3 71.0 + - - +
99E LYS* 3.7 23.8 + - - +
157E LEU* 6.1 0.2 - - - -
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Residues in contact with PHE 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C PRO* 3.7 28.0 - - + -
91E THR* 3.9 10.3 - - + -
92E ALA 3.4 2.7 - - - -
93E VAL* 3.8 14.1 - - + -
97E GLU* 1.3 75.2 - - - +
99E LYS* 1.3 67.3 + - - +
153E GLN* 3.4 47.3 - - + -
154E PHE* 3.5 43.5 - + - -
157E LEU* 4.2 12.8 - - + -
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Residues in contact with LYS 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E THR* 3.5 6.0 - - - +
92E ALA* 2.8 35.5 + - - +
94E ILE* 4.2 37.5 - - + -
97E GLU* 4.1 32.7 + - - +
98E PHE* 1.3 80.3 + - - +
100E GLU* 1.3 67.1 + - - +
101E LEU* 3.5 0.5 + - - +
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Residues in contact with GLU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E GLY 3.5 9.6 - - - +
91E THR* 4.8 2.2 - - - +
99E LYS* 1.3 74.9 - - - +
101E LEU* 1.3 62.1 + - - +
105E ASP* 4.3 3.5 - - - +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E TRP* 3.6 27.9 - - + -
89E GLU* 3.1 3.3 - - - +
90E GLY 2.8 36.5 + - - +
92E ALA* 4.0 27.4 - - + -
94E ILE* 4.0 16.4 - - + -
99E LYS 4.4 0.4 - - - +
100E GLU* 1.3 75.7 - - - +
102E LYS* 1.3 63.3 + - - +
105E ASP* 3.5 18.6 - - + +
106E TYR* 3.8 30.1 - - + +
146E VAL* 4.2 6.7 - - + -
175E PRO* 4.1 12.6 - - + -
177E LEU* 4.5 2.7 - - + -
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Residues in contact with LYS 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E TYR* 3.5 22.4 - - + +
88E TRP* 3.3 21.5 - - - +
89E GLU* 3.7 6.3 - - + +
101E LEU* 1.3 77.3 - - - +
103E LEU* 1.3 67.2 + - - +
104E THR* 3.2 23.1 - - - +
105E ASP* 2.6 52.0 + - - +
106E TYR* 3.8 6.1 - - - -
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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