Contacts of the strand formed by residues 99 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A SER* 5.9 4.9 - - - -
92A ILE 3.3 5.6 - - - +
93A GLN* 3.3 31.1 - - + +
97A GLY 3.5 7.2 + - - +
98A ARG* 1.3 76.4 - - - +
100A PHE* 1.3 67.7 + - - +
250B SER* 5.6 1.9 - - - -
251B ALA* 4.0 22.1 + - + +
252B ASP* 4.0 21.9 - - - +
255B LYS* 2.8 26.5 + - - +
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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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91A SER* 3.3 7.1 - - - -
92A ILE* 2.8 41.1 + - + +
94A LEU* 3.7 35.2 - - + -
98A ARG* 3.5 40.2 - - + -
99A GLU* 1.3 79.4 - - - +
101A ASP* 1.3 63.6 + - - +
118A ILE* 3.5 29.6 - - + -
119A GLN 3.8 4.9 - - - -
120A ASN 3.5 22.4 - - - -
121A PRO* 4.1 1.1 - - + -
122A SER* 4.0 17.3 - - - -
124A LEU* 4.0 6.5 - - + -
255B LYS* 6.1 3.8 - - - -
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Residues in contact with ASP 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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89A LYS* 5.4 6.8 - - - +
90A ILE 3.3 18.9 + - - +
91A SER* 4.5 4.6 - - - +
100A PHE* 1.3 77.8 - - - +
102A ALA* 1.3 62.0 + - - +
118A ILE* 3.5 5.5 - - - -
119A GLN* 2.8 44.2 + - + -
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Residues in contact with ALA 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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90A ILE* 2.9 38.4 + - + +
92A ILE* 3.6 30.5 - - + -
101A ASP* 1.3 78.4 - - - +
103A LYS* 1.3 66.7 + - - +
116A LEU* 4.4 8.5 - - + -
117A GLN 3.3 15.0 - - - +
118A ILE* 4.5 3.1 - - + -
119A GLN* 4.4 1.1 - - - -
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Residues in contact with LYS 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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90A ILE* 5.2 0.7 - - - -
102A ALA* 1.3 78.8 - - - +
104A LEU* 1.3 66.1 + - - +
105A ILE* 3.4 7.0 + - + +
116A LEU* 3.4 5.9 - - - -
117A GLN* 2.9 32.3 + - - +
119A GLN* 3.5 37.9 + - + +
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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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84A ILE* 3.9 31.0 - - + +
90A ILE* 4.5 14.4 - - + +
103A LYS* 1.3 72.6 - - - +
105A ILE* 1.3 63.4 + - - +
106A GLY* 3.4 30.5 - - - +
107A SER* 4.4 12.6 - - - +
114A ALA* 4.2 6.3 - - + -
115A LEU 3.5 8.3 - - - +
116A LEU* 4.2 8.9 - - + +
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Residues in contact with ILE 105 (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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76A TYR* 4.3 12.1 - - + +
103A LYS* 3.4 6.7 + - + +
104A LEU* 1.3 77.5 - - - +
106A GLY* 1.3 58.9 + - - +
115A LEU* 2.8 28.4 + - + +
116A LEU 4.1 2.9 - - - -
117A GLN* 3.5 49.8 - - + +
231A LEU 3.4 23.8 - - - +
232A ILE* 4.6 4.3 - - - +
235A GLY* 3.8 14.7 - - - +
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Residues in contact with GLY 106 (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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104A LEU* 3.4 12.7 - - - +
105A ILE* 1.3 82.2 - - - +
107A SER* 1.3 59.6 + - - -
115A LEU* 2.8 29.2 + - - +
231A LEU* 3.7 19.9 - - - +
235A GLY 3.9 8.1 - - - -
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Residues in contact with SER 107 (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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81A ASN* 3.3 26.1 + - - -
84A ILE* 5.1 0.2 - - - -
104A LEU* 4.4 13.8 - - - +
106A GLY* 1.3 74.8 - - - -
108A ASP* 1.3 60.2 + - - +
109A ASP* 4.2 7.9 + - - +
113A ILE 3.3 10.3 - - - -
114A ALA* 4.0 8.7 - - - -
231A LEU* 3.5 11.8 - - - +
235A GLY 4.9 0.4 + - - -
236A GLU* 5.3 1.2 - - - -
237A ILE* 3.7 14.7 - - - +
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Residues in contact with ASP 108 (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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81A ASN* 3.9 4.3 - - - +
107A SER* 1.3 72.0 - - - +
109A ASP* 1.3 57.5 + - - +
110A GLN* 3.2 12.0 + - - +
111A SER* 2.6 28.8 + - - +
112A ASP* 3.0 26.3 + - - -
113A ILE* 2.7 21.5 + - + +
227A LEU* 3.7 3.1 - - + +
231A LEU* 5.6 0.4 - - + -
237A ILE* 3.9 26.5 - - + +
239A ARG* 2.9 44.6 + - - -
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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