Contacts of the strand formed by residues 84 - 98 (chain N) in PDB entry 1H2I
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 TRP 84 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26N PHE* 3.9 4.5 - - - -
72N ILE* 4.3 15.9 - - + -
75N ALA* 3.5 28.7 - - + -
76N ASN* 2.9 26.3 + - - +
79N PHE* 3.9 11.0 - + + -
80N GLY 3.5 15.9 - - - -
81N TYR 4.3 5.0 - - - +
82N ASN 3.6 1.1 - - - -
83N GLY* 1.3 80.2 + - - +
85N ALA* 1.3 77.9 + - - +
86N HIS* 3.8 16.8 - + - -
113N VAL* 4.2 10.8 - - + -
114N GLN 3.1 10.3 - - - +
115N LEU* 3.9 14.1 - - + -
151N LEU* 3.9 27.4 - - + -
155N LEU* 4.2 9.9 - - + -
119O SER* 4.9 2.8 - - - -
120O TYR 4.4 0.2 - - - +
121O HIS* 3.4 39.3 + + - -
157O SER* 3.9 15.9 - - - -
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Residues in contact with ALA 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N PHE* 3.6 13.7 - - + -
84N TRP* 1.3 78.5 - - - +
86N HIS* 1.3 59.3 + - - +
113N VAL* 3.1 8.8 - - - +
114N GLN 2.7 30.2 + - - +
120O TYR* 2.9 55.4 - - + +
121O HIS* 3.9 3.1 - - - -
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Residues in contact with HIS 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N TRP* 3.8 4.5 - + + -
85N ALA* 1.3 79.6 - - - +
87N SER* 1.3 63.9 + - - +
88N ILE* 5.5 0.4 - - + -
111N VAL* 3.9 19.3 - - + -
112N ARG 3.1 11.9 - - - +
113N VAL* 4.0 3.6 - - - -
147N VAL* 5.2 6.4 - - + +
151N LEU* 3.8 37.7 - - + +
120O TYR* 3.2 15.3 + - - -
121O HIS* 2.9 42.6 - + + -
122O GLU 3.0 47.4 + - - -
123O ASP* 4.8 6.6 + - - -
154O ALA* 6.1 0.2 - - - -
157O SER* 3.5 18.2 - - - -
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Residues in contact with SER 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N HIS* 1.3 77.0 - - - +
88N ILE* 1.3 65.2 + - - +
89N THR* 4.5 6.9 - - - +
111N VAL* 3.4 8.0 - - - +
112N ARG* 2.9 43.7 + - - +
112O ARG* 5.3 5.4 - - - -
120O TYR* 4.0 17.1 + - - -
122O GLU* 3.4 17.7 - - - -
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Residues in contact with ILE 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N HIS* 5.5 0.4 - - + -
87N SER* 1.3 74.6 - - - +
89N THR* 1.3 64.6 + - - +
90N GLN* 3.7 27.9 - - - +
91N GLN* 4.2 3.6 - - + +
109N ALA* 4.9 5.2 - - + -
110N PHE 3.5 5.4 - - - +
111N VAL* 4.6 6.7 - - + +
147N VAL* 3.9 26.9 - - + -
110O PHE* 3.7 34.1 - - + -
122O GLU* 2.9 29.5 + - + +
123O ASP* 3.7 32.5 - - - +
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Residues in contact with THR 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87N SER* 3.7 6.7 + - - +
88N ILE* 1.3 73.9 - - - +
90N GLN* 1.3 64.2 + - - +
110N PHE* 2.8 23.9 + - - +
112N ARG* 3.9 28.7 - - + -
122N GLU* 2.6 30.9 + - - +
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Residues in contact with GLN 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N ILE* 3.1 10.1 - - - +
89N THR* 1.3 88.0 + - - +
91N GLN* 1.3 66.0 + - - +
92N ASN* 3.7 33.9 - - - +
109N ALA* 3.4 1.2 - - - -
110N PHE* 2.8 46.8 + - + -
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Residues in contact with GLN 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N ILE* 4.2 4.2 - - + +
90N GLN* 1.3 81.8 + - - +
92N ASN* 1.3 64.7 + - - +
93N VAL 4.2 0.7 + - - -
107N VAL* 3.6 17.9 - - + +
108N CYS 3.2 13.9 - - - +
109N ALA* 4.0 2.8 - - + +
143N ARG* 2.9 69.6 + - - +
146N ALA* 3.8 5.1 - - - +
147N VAL* 3.6 14.8 - - - +
110O PHE* 3.3 36.8 - - + -
124O VAL* 3.9 0.9 - - - +
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Residues in contact with ASN 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M ARG* 5.6 3.3 + - - +
90N GLN* 3.7 23.5 - - - +
91N GLN* 1.3 77.7 + - - +
93N VAL* 1.3 80.1 + - - +
94N ASP* 3.3 11.7 + - - +
107N VAL* 4.4 2.0 - - - -
108N CYS* 2.9 49.5 + - - -
110N PHE* 5.7 0.2 - - - -
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Residues in contact with VAL 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91N GLN 4.2 0.2 + - - -
92N ASN* 1.3 80.1 + - - +
94N ASP* 1.3 63.3 + - - +
95N PHE* 3.8 13.7 - - - +
96N VAL* 3.9 24.5 - - + -
107N VAL* 3.8 23.8 - - + -
139N LEU* 4.4 7.9 - - + -
143N ARG* 3.6 37.9 - - - +
94O ASP* 5.3 0.7 - - - +
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Residues in contact with ASP 94 (chain N).
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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93M VAL* 5.7 0.2 - - - -
139M LEU* 3.6 13.9 - - + +
143M ARG* 2.6 34.9 + - - -
92N ASN* 3.3 19.1 + - - +
93N VAL* 1.3 73.4 - - - +
95N PHE* 1.3 71.1 + - + +
106N GLY 2.8 17.5 + - - +
126N TYR* 2.6 30.8 + - - +
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Residues in contact with PHE 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135M LYS* 3.9 38.8 - - + +
136M ALA* 3.6 37.0 - - + -
139M LEU* 4.0 8.1 - - + -
93N VAL* 3.5 4.2 - - - +
94N ASP* 1.3 90.6 - - + +
96N VAL* 1.3 70.8 + - - +
97N ASP* 3.5 19.7 - - - +
104N TYR* 3.2 34.3 - - + -
105N VAL* 3.4 5.0 - - - +
106N GLY* 3.3 36.0 + - - +
126N TYR* 4.0 5.4 - - - -
130N GLU* 5.7 0.7 - - + -
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Residues in contact with VAL 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93N VAL* 3.9 18.2 - - + -
95N PHE* 1.3 80.6 - - - +
97N ASP* 1.3 65.1 + - - +
98N LEU 4.3 0.3 + - - -
103N PHE* 4.2 21.5 - - + -
104N TYR 3.6 2.9 - - - -
105N VAL* 4.2 9.9 - - + -
135N LYS* 4.3 24.0 - - + -
139N LEU* 4.0 24.0 - - + -
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Residues in contact with ASP 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135M LYS* 2.9 34.1 + - - +
95N PHE* 3.5 14.7 - - - +
96N VAL* 1.3 84.2 + - - +
98N LEU* 1.3 59.8 + - - +
99N ASN* 3.9 18.8 - - - +
102N LYS 3.6 0.5 - - - +
103N PHE* 3.1 8.3 - - - -
104N TYR* 2.7 51.4 + - + +
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Residues in contact with LEU 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96N VAL 4.3 0.8 + - - -
97N ASP* 1.3 71.8 - - - +
99N ASN* 1.3 66.4 + - - +
100N ASN 3.9 18.8 - - - +
101N GLY* 4.0 12.6 - - - +
102N LYS 3.3 13.2 - - - +
103N PHE* 3.8 33.4 - - + -
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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