Contacts of the strand formed by residues 99 - 108 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D ARG* 5.9 2.1 + - - -
91D SER* 5.8 6.1 - - - -
92D ILE 3.3 7.0 - - - +
93D GLN* 3.4 28.7 - - + +
97D GLY 3.5 4.8 + - - +
98D ARG* 1.3 76.4 - - - +
100D PHE* 1.3 69.9 + - - +
250E SER* 5.5 1.9 - - - -
251E ALA* 3.8 26.6 + - + +
252E ASP* 4.1 18.9 - - - +
255E LYS* 2.8 34.2 + - - +
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Residues in contact with PHE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D SER* 3.3 6.7 - - - -
92D ILE* 2.8 39.2 + - + +
94D LEU* 3.7 33.9 - - + -
98D ARG* 3.5 39.5 - - + -
99D GLU* 1.3 80.4 - - - +
101D ASP* 1.3 62.4 + - - +
118D ILE* 3.5 34.3 - - + -
119D GLN 3.8 4.5 - - - +
120D ASN 3.5 23.6 - - - -
121D PRO* 4.1 1.8 - - + -
122D SER* 4.0 17.0 - - - -
124D LEU* 4.0 6.7 - - + -
255E LYS* 6.3 0.9 - - - -
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Residues in contact with ASP 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LYS* 5.4 6.4 - - - +
90D ILE 3.3 18.5 + - - +
91D SER* 5.1 4.9 - - - -
100D PHE* 1.3 76.9 - - - +
102D ALA* 1.3 61.8 + - - +
118D ILE* 3.5 5.0 - - - -
119D GLN* 2.8 43.7 + - + -
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 2.9 37.0 + - + +
92D ILE* 3.6 30.5 - - + -
101D ASP* 1.3 79.6 - - - +
103D LYS* 1.3 68.0 + - - +
116D LEU* 4.3 8.7 - - + -
117D GLN 3.3 14.6 - - - +
118D ILE* 4.5 3.4 - - + -
119D GLN* 4.4 1.1 - - - -
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Residues in contact with LYS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 5.0 0.9 - - - -
102D ALA* 1.3 77.5 - - - +
104D LEU* 1.3 66.0 + - - +
105D ILE* 3.4 7.8 + - + +
116D LEU* 3.3 5.2 - - - -
117D GLN 2.8 30.8 + - - +
119D GLN* 3.5 39.8 + - + +
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ILE* 3.9 24.9 - - + +
90D ILE* 4.5 11.9 - - + +
103D LYS* 1.3 74.4 - - - +
105D ILE* 1.3 62.1 + - - +
106D GLY* 3.5 30.7 - - - +
107D SER* 4.4 12.3 - - - +
114D ALA* 4.2 4.5 - - + -
115D LEU 3.5 9.4 - - - +
116D LEU* 3.7 19.2 - - + +
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Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TYR* 4.3 7.2 - - + -
103D LYS* 3.4 6.7 + - + +
104D LEU* 1.3 76.5 - - - +
106D GLY* 1.3 58.6 + - - +
115D LEU* 2.8 33.7 + - + +
116D LEU 4.0 2.9 - - - -
117D GLN* 3.5 50.0 - - + +
231D LEU 3.4 25.1 - - - +
232D ILE* 4.6 4.0 - - - +
235D GLY* 3.9 14.2 - - - +
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Residues in contact with GLY 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 3.5 10.8 - - - +
105D ILE* 1.3 81.5 - - - +
107D SER* 1.3 59.4 + - - -
115D LEU* 2.8 30.3 + - - +
231D LEU* 3.6 21.0 - - - +
235D GLY 4.1 8.5 - - - -
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ASN* 3.3 24.7 + - - -
84D ILE* 5.1 0.4 - - - -
104D LEU* 4.4 14.7 - - - +
106D GLY* 1.3 75.2 - - - -
108D ASP* 1.3 60.3 + - - +
109D ASP* 4.2 8.2 + - - +
113D ILE 3.3 11.4 - - - -
114D ALA* 4.0 8.3 - - - -
231D LEU* 3.6 14.4 - - - +
235D GLY 5.2 0.2 + - - -
236D GLU* 5.3 2.3 - - - +
237D ILE* 5.0 5.2 + - - +
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Residues in contact with ASP 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ASN* 3.9 4.0 - - - +
107D SER* 1.3 73.4 - - - +
109D ASP* 1.3 58.4 + - - +
110D GLN* 3.2 11.3 + - - +
111D SER* 2.6 30.3 + - - +
112D ASP* 2.9 25.8 + - - -
113D ILE* 2.7 20.8 + - + +
227D LEU* 3.7 4.3 - - + +
231D LEU* 5.7 0.4 - - + -
237D ILE* 3.9 23.4 - - + +
239D ARG* 2.9 44.4 + - - -
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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