Contacts of the strand formed by residues 119 - 134 (chain C) in PDB entry 2IUO
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 GLY 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C VAL* 4.7 1.1 - - - +
113C HIS* 3.4 7.8 - - - -
117C GLY 3.5 1.4 + - - -
118C ASP* 1.3 82.7 + - - +
120C ILE* 1.3 60.2 + - - -
150C TYR* 4.2 4.5 - - - -
151C LEU 3.4 11.2 - - - -
153C THR* 3.4 18.4 - - - -
93H THR* 2.7 28.2 + - - +
81I ARG* 5.6 0.7 - - - -
124I ILE* 4.5 0.4 - - - -
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C VAL* 4.8 1.3 - - - -
119C GLY* 1.3 77.9 - - - +
121C ILE* 1.3 62.8 + - - +
122C GLY* 3.9 9.9 - - - -
150C TYR* 3.4 8.2 - - - -
151C LEU* 2.9 55.1 + - + -
1157C BR 3.5 19.3 - - + -
1158C CL 3.9 0.4 - - + -
92H PRO* 3.8 32.1 - - + +
93H THR* 3.8 8.5 - - - +
96H ARG* 3.4 33.7 - - + +
124I ILE* 3.9 25.1 - - + -
1157I BR 4.0 4.9 - - + -
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C VAL* 3.7 26.5 - - + +
116C PHE* 4.1 12.1 - - + -
120C ILE* 1.3 73.2 - - - +
122C GLY* 1.3 67.6 + - - +
148C GLY* 3.8 25.6 - - - +
149C LYS 3.7 0.4 - - - -
150C TYR* 3.7 35.2 - - + +
93H THR* 4.8 3.4 + - - +
96H ARG* 3.2 25.0 - - - +
97H PHE* 4.5 12.0 - - + -
100H MET* 4.1 10.2 - - + +
142H ALA* 3.6 31.6 - - + -
144H ILE* 4.6 10.3 - - + -
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Residues in contact with GLY 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ILE* 3.8 7.1 + - - +
121C ILE* 1.3 74.5 - - - +
123C ALA* 1.3 59.7 + - - -
124C ILE 3.4 2.9 - - - -
125C ASN* 4.4 4.9 - - - -
126C PHE* 3.5 22.2 - - - +
148C GLY* 3.7 7.4 - - - -
149C LYS* 2.9 19.8 + - - -
151C LEU* 5.1 3.1 - - - -
1157C BR 3.7 2.7 - - - -
1158C CL 3.5 15.3 - - - -
100H MET* 3.9 2.5 - - - +
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE 3.7 1.4 + - - -
122C GLY* 1.3 70.6 - - - -
124C ILE* 1.3 66.6 + - - +
126C PHE* 3.5 24.1 - - - +
1158C CL 3.1 5.7 - - - +
96H ARG* 3.7 30.0 - - + +
99H GLU* 3.6 24.9 - - + +
100H MET* 4.0 13.7 - - + +
103H VAL* 5.8 3.9 - - + +
104H TYR* 5.6 2.1 - - - -
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Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ARG* 6.2 2.9 - - - +
122C GLY 3.4 0.6 - - - -
123C ALA* 1.3 85.8 - - - +
125C ASN* 1.3 63.4 + - - +
126C PHE* 2.9 12.1 + - - +
1157C BR 4.3 0.9 - - + -
1158C CL 3.6 18.1 - - + +
99H GLU* 4.4 2.5 - - - +
103H VAL* 6.3 1.3 - - + -
119I GLY* 4.6 0.7 - - - -
120I ILE* 3.9 30.7 - - + -
151I LEU* 3.4 27.6 - - + +
152I PRO 3.3 26.6 - - - +
153I THR* 3.6 28.0 + - - +
154I LYS 5.5 0.5 + - - -
92J PRO* 4.3 15.3 - - + -
96J ARG* 4.1 3.6 - - - +
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Residues in contact with ASN 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C GLY* 3.9 5.8 - - - +
124C ILE* 1.3 74.9 - - + +
126C PHE* 1.3 61.9 + - - +
148C GLY* 3.5 0.2 - - - -
149C LYS* 3.1 59.8 + - + +
151C LEU* 6.0 2.2 - - + +
135H ASP* 4.7 1.2 + - - -
137H GLU* 5.0 8.6 + - - +
141H ARG* 2.9 23.3 + - - +
151I LEU* 5.5 9.9 - - + +
152I PRO 5.0 4.7 - - - +
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Residues in contact with PHE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 5.7 0.2 - - + -
122C GLY 3.5 22.0 - - - +
123C ALA* 3.5 23.6 - - - +
124C ILE 2.9 8.9 + - - +
125C ASN* 1.3 79.1 + - - +
127C LYS* 1.3 84.7 + - - +
128C LEU* 3.9 13.7 - - + -
146C LEU* 3.8 18.8 - - + -
147C ASP 3.2 20.0 - - - -
148C GLY* 4.0 0.9 - - - -
100H MET* 3.5 41.7 - - + -
104H TYR* 3.8 32.2 + + - -
141H ARG* 3.9 2.9 - - - +
156I PHE* 4.2 12.6 - - - -
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Residues in contact with LYS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 1.3 85.3 - - - +
128C LEU* 1.3 70.9 + - - +
129C ASP* 4.4 21.7 + - - +
147C ASP* 2.9 58.0 + - + +
141H ARG* 5.2 2.5 - - - +
156I PHE* 3.9 35.7 - - + -
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Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA* 3.8 21.3 - - + +
126C PHE* 3.9 11.7 - - + -
127C LYS* 1.3 81.5 - - - +
129C ASP* 1.3 68.1 + - - +
130C VAL* 5.6 1.1 - - + -
144C ILE* 4.7 2.2 - - + -
145C THR 3.3 12.1 - - - +
146C LEU* 4.1 12.8 - - + -
100H MET* 6.2 1.1 - - + -
104H TYR* 3.4 55.4 - - + -
107H THR* 5.7 1.1 - - + -
108H LEU* 3.7 42.2 - - + -
156I PHE* 4.2 8.9 - - + -
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Residues in contact with ASP 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA* 5.4 3.1 - - - -
127C LYS* 4.4 19.4 + - - +
128C LEU* 1.3 78.7 - - - +
130C VAL* 1.3 66.3 + - - +
131C LYS* 3.0 46.0 - - - +
143C VAL 3.8 0.7 - - - +
144C ILE* 3.3 6.6 - - - +
145C THR* 3.0 48.4 + - - +
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Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU* 5.6 1.8 - - + -
129C ASP* 1.3 81.1 - - - +
131C LYS* 1.3 63.7 + - - +
142C ALA* 4.4 6.7 - - + -
143C VAL 3.7 2.2 - - - -
144C ILE* 4.1 15.3 - - + +
108H LEU* 3.8 28.9 - - + -
111H LEU* 4.5 22.6 - - + +
112H VAL* 4.6 10.8 - - + +
115H LYS* 3.4 37.0 + - + +
116H PHE* 4.0 26.5 - - + -
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ASP* 3.0 28.0 - - - +
130C VAL* 1.3 74.9 - - - +
132C LYS* 1.3 63.5 - - - +
133C VAL* 3.8 9.3 + - + +
142C ALA* 3.4 4.5 - - - -
143C VAL* 2.9 40.9 + - + +
145C THR* 5.9 1.3 - - - +
115H LYS* 5.5 0.4 - - - +
116H PHE* 4.4 3.4 - - - -
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Residues in contact with LYS 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C VAL 4.4 0.2 + - - -
131C LYS* 1.3 73.9 - - - +
133C VAL* 1.3 68.3 + - - +
134C ALA 5.0 0.7 - - - +
140C GLU* 3.2 42.3 + - + +
141C ARG 3.5 4.9 - - - +
115H LYS* 2.9 37.4 + - + +
116H PHE* 3.7 24.5 - - + +
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C LYS* 4.2 11.2 - - + +
132C LYS* 1.3 82.6 - - - +
134C ALA* 1.3 79.4 + - - +
140C GLU* 3.8 0.2 - - - -
141C ARG* 2.9 38.1 + - + +
143C VAL* 3.8 29.4 - - + -
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Residues in contact with ALA 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LYS* 4.3 1.6 - - - +
133C VAL* 1.3 88.2 - - - +
135C ASP* 1.3 65.4 + - - +
136C PRO* 3.6 8.3 - - - +
139C GLY 3.8 7.0 - - - +
140C GLU* 4.7 5.8 - - + +
141C ARG* 4.9 1.4 - - - +
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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