Contacts of the strand formed by residues 96 - 106 (chain A) in PDB entry 2I9W
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 ASP 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLU 3.5 4.5 + - - +
95A THR* 1.3 71.5 - - - +
97A TRP* 1.3 68.3 + - - +
98A ALA* 4.3 0.2 - - - +
122A PHE* 3.2 3.4 - - - +
123A LYS* 2.8 64.7 + - - +
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Residues in contact with TRP 97 (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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60A TYR* 3.8 21.5 - + - +
63A PHE* 3.8 23.9 + + + -
64A VAL* 3.7 43.5 - - + +
91A TRP* 3.4 45.1 - + - -
92A ALA* 2.9 24.0 + - - -
95A THR* 3.2 45.7 + - + -
96A ASP* 1.3 80.5 + - - +
98A ALA* 1.3 57.7 + - - +
99A GLY 3.8 0.2 - - - -
120A ALA* 4.2 20.6 - - + -
121A TYR 3.7 13.2 - - - -
122A PHE* 4.3 0.2 - - - +
131A HIS* 4.5 11.2 - + - -
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Residues in contact with ALA 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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12A ILE* 3.7 15.8 - - - +
14A PRO* 3.7 13.7 - - - +
97A TRP* 1.3 74.4 - - - +
99A GLY* 1.3 59.0 + - - +
121A TYR* 2.9 23.3 + - + +
122A PHE* 4.0 4.5 - - - -
123A LYS* 4.2 7.9 - - + -
128A LEU* 3.8 30.0 - - + +
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Residues in contact with GLY 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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12A ILE* 3.1 20.6 - - - -
14A PRO* 4.0 2.9 - - - -
60A TYR* 3.0 25.5 + - - -
98A ALA* 1.3 80.2 - - - +
100A LEU* 1.3 57.0 + - - -
120A ALA* 3.6 1.6 - - - -
121A TYR* 2.8 34.0 + - - -
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Residues in contact with LEU 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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10A CYS* 4.1 27.0 - - + +
12A ILE 2.8 9.3 + - - +
13A ASN* 3.3 25.1 + - - +
14A PRO* 4.3 0.2 - - - +
56A MSE 5.2 3.8 - - + +
57A ARG* 3.9 31.2 - - + +
60A TYR* 4.0 39.2 - - + -
99A GLY* 1.3 73.2 - - - +
101A GLU* 1.3 65.3 + - - +
102A VAL* 4.0 10.3 + - + -
118A PHE* 3.7 30.7 - - + -
119A LYS 3.5 15.7 - - - +
120A ALA* 4.5 0.9 - - - -
121A TYR* 4.3 1.7 - - - -
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Residues in contact with GLU 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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13A ASN* 3.7 21.5 - - - +
15A ALA* 3.5 17.4 - - - +
100A LEU* 1.3 73.2 - - - +
102A VAL* 1.3 71.9 + - - +
103A VAL* 3.4 11.0 + - + +
118A PHE* 3.2 4.9 - - - +
119A LYS* 2.8 55.6 + - + +
121A TYR* 2.5 37.7 + - + -
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Residues in contact with VAL 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 ASN* 5.2 1.4 - - - +
53A GLU* 3.9 25.8 - - + +
56A MSE 6.3 1.8 - - + -
57A ARG* 3.7 39.3 - - + +
100A LEU* 4.0 19.2 - - + -
101A GLU* 1.3 75.3 - - - +
103A VAL* 1.3 64.8 + - - +
104A ALA 4.0 11.9 - - - +
105A HIS* 5.1 0.2 - - + -
116A VAL* 4.1 15.5 - - + -
117A GLU 3.9 9.9 - - - +
118A PHE* 4.1 6.1 - - + -
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLU* 4.1 21.3 - - + +
102A VAL* 1.3 77.0 - - - +
104A ALA* 1.3 61.1 + - + +
117A GLU* 2.8 48.3 + - + +
118A PHE* 4.2 6.5 - - - -
119A LYS* 4.3 24.2 - - + -
132A HIS* 4.6 0.4 - - - +
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Residues in contact with ALA 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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102A VAL* 3.6 5.0 - - - +
103A VAL* 1.3 83.4 - - + +
105A HIS* 1.3 62.7 + - - +
106A THR* 5.3 4.3 - - - +
115A GLN 4.8 0.2 - - - -
116A VAL* 3.4 5.4 - - - +
117A GLU* 2.9 49.6 + - + +
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Residues in contact with HIS 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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51A THR* 4.0 20.6 - - + -
52A ALA* 4.1 10.5 + - + +
53A GLU* 3.5 56.5 + - + +
102A VAL* 5.1 0.9 - - + -
104A ALA* 1.3 75.6 - - - +
106A THR* 1.3 72.4 + - - +
107A PRO* 3.4 40.7 - - + +
114A ALA* 4.7 0.2 - - - +
115A GLN 3.4 11.7 - - - -
116A VAL* 3.9 4.5 - - + +
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Residues in contact with THR 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 ALA* 5.3 5.2 - - - +
105A HIS* 1.3 76.2 + - - +
107A PRO* 1.3 63.6 - - - +
108A LYS 3.2 3.6 - - - +
109A LEU* 3.7 35.4 + - + +
114A ALA* 3.2 3.1 - - - -
115A GLN* 2.8 44.4 + - - +
134A LEU* 6.1 0.2 - - - +
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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