Contacts of the strand formed by residues 99 - 108 (chain F) in PDB entry 3STJ
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 99 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250D SER* 5.5 1.6 - - - -
251D ALA* 3.6 27.5 + - + +
252D ASP* 4.0 20.4 - - - +
255D LYS* 2.8 37.2 + - - +
30F ARG* 6.2 1.8 - - - -
91F SER* 5.8 5.6 - - - -
92F ILE 3.3 6.5 - - - +
93F GLN* 3.3 28.6 - - + +
97F GLY 3.5 4.1 + - - +
98F ARG* 1.3 76.7 - - - +
100F PHE* 1.3 67.5 + - - +
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Residues in contact with PHE 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D LYS* 5.1 1.1 - - - +
91F SER* 3.3 6.5 - - - -
92F ILE* 2.8 41.0 + - + +
94F LEU* 3.7 34.5 - - + -
98F ARG* 3.5 40.6 - - + -
99F GLU* 1.3 79.1 - - - +
101F ASP* 1.3 63.2 + - - +
118F ILE* 3.5 29.6 - - + -
119F GLN 3.8 4.5 - - - -
120F ASN 3.5 22.4 - - - -
121F PRO* 4.1 1.6 - - + -
122F SER* 3.9 17.0 - - - -
124F LEU* 4.0 6.3 - - + -
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Residues in contact with ASP 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F LYS* 5.4 6.2 - - - +
90F ILE 3.3 19.2 + - - +
91F SER* 5.1 4.4 - - - -
100F PHE* 1.3 78.6 - - - +
102F ALA* 1.3 60.9 + - - +
118F ILE* 3.5 4.5 - - - -
119F GLN* 2.8 43.7 + - + -
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ILE* 2.9 38.1 + - + +
92F ILE* 3.6 31.2 - - + -
101F ASP* 1.3 79.2 - - - +
103F LYS* 1.3 65.7 + - - +
116F LEU* 4.4 9.0 - - + -
117F GLN 3.3 14.8 - - - +
118F ILE* 4.5 2.9 - - + -
119F GLN* 4.4 1.6 - - - -
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Residues in contact with LYS 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ILE* 5.2 0.7 - - - -
102F ALA* 1.3 78.5 - - - +
104F LEU* 1.3 67.4 + - - +
105F ILE* 3.3 7.8 + - + +
116F LEU* 3.3 5.1 - - - -
117F GLN* 2.9 31.0 + - - -
119F GLN* 3.5 39.4 + - + +
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Residues in contact with LEU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F ILE* 4.0 25.6 - - + +
90F ILE* 4.5 11.6 - - + +
103F LYS* 1.3 72.7 - - - +
105F ILE* 1.3 63.3 + - - +
106F GLY* 3.4 30.5 - - - +
107F SER* 4.4 11.9 - - - +
114F ALA* 4.1 5.2 - - + -
115F LEU 3.5 8.7 - - - +
116F LEU* 3.8 19.4 - - + +
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Residues in contact with ILE 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F TYR* 4.3 11.7 - - + -
103F LYS* 4.2 6.1 - - + +
104F LEU* 1.3 78.6 - - - +
106F GLY* 1.3 59.2 + - - +
115F LEU* 2.8 29.1 + - + +
116F LEU 4.1 2.5 - - - -
117F GLN* 3.5 49.6 - - + +
231F LEU 3.5 24.7 - - - +
232F ILE* 4.6 3.8 - - - +
235F GLY* 3.8 14.8 - - - +
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Residues in contact with GLY 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F LEU* 3.4 11.6 - - - +
105F ILE* 1.3 81.9 - - - +
107F SER* 1.3 59.1 + - - -
115F LEU* 2.8 30.9 + - - +
231F LEU* 3.6 20.5 - - - +
235F GLY 3.9 8.1 - - - -
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Residues in contact with SER 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F ASN* 3.3 24.8 + - - -
84F ILE* 5.1 0.4 - - - -
104F LEU* 4.4 14.3 - - - +
106F GLY* 1.3 74.6 - - - -
108F ASP* 1.3 60.1 + - - +
109F ASP* 4.2 8.7 + - - +
113F ILE 3.3 11.0 - - - -
114F ALA* 4.0 9.2 - - - +
231F LEU* 3.6 14.1 - - - +
235F GLY 5.0 0.4 + - - -
236F GLU* 5.5 1.2 - - - -
237F ILE* 5.2 4.5 + - - +
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Residues in contact with ASP 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F ASN* 3.9 4.0 - - - +
107F SER* 1.3 71.6 - - - +
109F ASP* 1.3 58.2 + - - +
110F GLN* 3.2 13.2 + - - +
111F SER* 2.6 30.0 + - - +
112F ASP* 3.0 26.0 + - - -
113F ILE* 2.7 22.4 + - + +
227F LEU* 3.7 4.9 - - + +
231F LEU* 5.6 0.2 - - + -
237F ILE* 4.0 23.3 - - + +
239F ARG* 3.2 39.0 + - - -
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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