Contacts of the strand formed by residues 79 - 90 (chain B) in PDB entry 1JJ2
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 MET 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B GLY 4.4 2.9 - - - +
41B PHE* 3.2 50.9 - - + -
42B ALA* 3.3 33.2 - - + +
77B PRO 4.1 2.0 - - - +
78B PRO* 1.3 78.0 - - - +
80B ARG* 1.3 73.7 + - - +
144B THR* 3.4 24.9 - - + -
145B HIS 3.4 12.3 - - - +
146B THR* 3.9 18.2 - - + +
147B VAL* 5.0 0.9 - - - -
162B MET* 5.1 2.9 - - - +
164B THR* 5.5 3.1 - - - +
187B GLU* 3.5 1.4 - - - -
188B HIS* 3.0 39.5 + - + +
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PRO* 5.4 1.1 - - + +
79B MET* 1.3 86.1 - - - +
81B ALA* 1.3 61.1 + - - +
82B VAL* 3.0 15.4 + - + +
104B GLU 5.5 3.3 + - - -
105B PHE 4.5 2.6 + - - -
106B HIS* 3.7 43.8 - - - +
144B THR* 4.3 1.6 - - - -
145B HIS* 3.1 49.9 + - + -
147B VAL* 4.6 13.7 - - + +
185B GLY 4.0 15.9 - - - +
186B GLY 3.5 3.8 - - - -
187B GLU* 3.8 30.1 + - + +
188B HIS* 3.8 2.0 - - - -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG* 1.3 67.8 - - - +
82B VAL* 1.3 63.2 + - - +
83B ALA 3.3 2.3 + - - -
142B LEU* 3.6 37.5 - - + -
143B ILE 3.4 7.9 - - - -
144B THR* 4.1 4.7 - - - +
181B ILE* 4.2 6.5 - - + -
182B VAL* 3.9 12.1 - - + +
185B GLY 4.1 1.0 - - - +
186B GLY* 3.0 36.6 + - - +
188B HIS* 3.5 10.7 - - + -
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG* 3.0 19.9 + - + +
81B ALA* 1.3 71.7 - - - +
83B ALA* 1.3 63.4 + - - +
101B TRP* 3.3 44.1 - - + -
102B THR* 3.7 11.9 + - - +
104B GLU 5.4 3.4 - - - +
105B PHE* 3.5 24.9 - - + -
109B LEU* 4.3 7.6 - - + -
113B LEU* 6.2 0.2 - - + -
143B ILE* 2.9 11.1 + - + +
144B THR 6.1 0.2 - - - -
145B HIS* 3.4 28.0 - - + +
182B VAL* 4.3 4.3 - - - -
185B GLY 5.1 4.0 - - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ALA 3.3 3.0 + - - -
82B VAL* 1.3 83.7 - - - +
84B LEU* 1.3 62.5 + - - +
99B GLU* 5.0 0.7 - - + -
100B VAL 3.1 15.7 - - - +
101B TRP* 3.4 35.2 - - + +
142B LEU* 3.2 9.4 - - - +
143B ILE* 2.8 38.5 + - + -
182B VAL* 3.7 8.4 - - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA* 1.3 72.2 - - - +
85B ARG* 1.3 68.7 + - - +
86B ALA* 4.8 1.3 - - + -
98B THR 3.9 0.3 - - - +
99B GLU* 3.3 4.3 - - - -
100B VAL* 2.9 40.3 + - + +
128B ILE* 3.7 27.1 - - + -
140B LEU* 4.2 13.9 - - + -
141B ARG 3.3 23.8 - - - +
142B LEU* 3.8 11.4 - - + -
166B VAL* 5.3 0.2 - - + -
175B LEU* 5.6 4.7 - - + +
178B ALA* 3.7 29.4 - - + -
179B LEU* 4.4 13.9 - - + -
182B VAL* 3.9 8.5 - - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26700 G 3.3 7.9 - - - +
26710 U 2.9 33.9 + - - +
26720 C 3.6 7.1 + - - -
28190 C 2.8 20.4 + - - -
83B ALA 4.0 1.6 - - - -
84B LEU* 1.3 78.0 - - - +
86B ALA* 1.3 67.0 + - - +
87B TYR* 3.4 35.6 + - + -
96B PRO* 3.9 18.5 - - + +
98B THR 3.6 7.4 - - - +
99B GLU* 2.6 38.5 + - + -
140B LEU* 4.0 1.0 - - - -
141B ARG 2.7 38.1 + - - +
142B LEU* 4.6 0.2 - - - +
143B ILE* 4.3 15.5 - - + +
163B GLU* 2.7 30.7 + - - -
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 3.9 0.4 + - + -
85B ARG* 1.3 74.4 - - - +
87B TYR* 1.3 55.7 + - - +
96B PRO* 3.5 2.9 - - - +
97B LEU* 2.5 39.8 + - + +
98B THR 2.9 10.1 + - - +
128B ILE* 3.4 37.5 - - + -
137B LEU* 4.1 8.3 - - + -
140B LEU* 4.1 18.2 - - + -
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26720 C 2.7 33.4 + - - -
26730 U 3.8 9.9 - - - -
85B ARG* 3.4 21.0 - - + -
86B ALA* 1.3 77.9 - - - +
88B GLU* 1.3 55.7 + - - +
94B GLN* 4.1 17.5 - - + -
95B ARG 3.3 25.6 - - - +
96B PRO* 3.6 11.4 - - + -
97B LEU* 4.5 1.3 - - - -
137B LEU* 3.3 9.2 - - - +
138B GLY* 2.5 31.1 + - - +
139B ASP* 3.5 34.8 + - - +
141B ARG* 3.6 19.7 - - + -
163B GLU* 2.4 38.6 + - - -
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B TYR* 1.3 75.9 - - - +
89B ASP* 1.3 70.7 + - - +
90B THR* 3.4 19.1 - - + +
94B GLN* 3.6 3.3 - - - -
95B ARG* 2.9 37.7 + - + +
96B PRO 5.4 0.9 - - - +
97B LEU* 4.0 31.0 - - + +
131B ALA* 5.7 0.4 - - + -
136B ASP* 3.0 22.0 - - + +
138B GLY* 4.6 0.4 - - - -
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Residues in contact with ASP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLU* 1.3 78.3 - - - +
90B THR* 1.3 63.7 + - - +
93B GLY 4.2 2.9 - - - -
94B GLN* 3.6 27.3 + - - +
135B GLY 5.1 2.6 - - - +
136B ASP* 2.7 28.4 + - - +
137B LEU 3.8 14.0 - - - +
138B GLY* 3.7 8.3 - - - -
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLU* 3.4 33.7 - - + +
89B ASP* 1.3 82.4 - - - +
91B PRO* 1.3 64.8 - - - +
92B TYR* 2.8 24.9 + - - +
93B GLY* 2.9 24.9 + - - +
95B ARG* 4.3 17.7 + - + -
144I THR* 2.7 24.9 + - - +
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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