Contacts of the strand formed by residues 115 - 124 (chain C) in PDB entry 2HU4
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 PHE 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ILE* 3.6 29.6 - - + -
105C SER* 5.7 0.2 + - - -
113C ASP 4.3 0.4 + - - -
114C VAL* 1.3 87.8 - - - +
116C VAL* 1.3 60.9 + - - +
117C ILE* 3.8 23.1 + - + +
133C PHE* 4.5 2.9 - + - -
135C THR* 4.1 20.9 - - + -
137C GLY* 5.1 1.6 - - - -
138C ALA 3.7 17.0 - - - -
139C LEU* 4.0 7.1 - - + +
140C LEU* 3.9 5.2 - - - +
159C MET* 3.7 31.4 - - + -
167C PRO* 2.8 17.6 + - - +
168C SER* 3.3 41.1 - - - -
169C PRO* 3.4 18.2 - - + -
171C SER* 4.2 4.7 - - - -
440C SER* 4.1 1.6 + - - -
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Residues in contact with VAL 116 (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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114C VAL 3.8 0.6 + - - -
115C PHE* 1.3 74.2 - - - +
117C ILE* 1.3 65.9 + - - +
135C THR* 3.4 1.0 - - - -
136C GLN* 3.1 46.7 + - + -
138C ALA* 2.9 34.9 + - + +
139C LEU* 4.1 5.4 - - - +
140C LEU* 4.1 13.0 - - + -
145C SER* 5.1 4.9 - - - +
148C THR* 4.0 14.6 - - + +
438C TRP* 5.6 1.1 - - + -
439C THR 3.4 23.3 - - - +
440C SER* 3.3 9.6 - - - +
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Residues in contact with ILE 117 (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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103C ASP* 5.9 2.5 - - - +
105C SER* 5.5 0.2 - - - +
115C PHE* 3.8 20.8 + - + +
116C VAL* 1.3 82.0 - - - +
118C ARG* 1.3 75.3 + - - +
120C PRO* 4.1 17.3 - - + -
131C THR* 6.2 0.4 - - + -
133C PHE* 3.6 45.3 - - + -
134C LEU 3.3 13.9 - - - +
135C THR* 4.0 2.5 - - - -
136C GLN* 5.0 1.3 - - - -
156C ARG* 4.6 1.8 - - - -
167C PRO* 4.2 16.6 - - + -
439C THR 3.9 1.5 - - - +
440C SER* 2.8 30.7 + - - +
441C GLY* 3.4 26.1 + - - +
442C SER 6.2 0.2 - - - -
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Residues in contact with ARG 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 1.3 86.0 - - - +
119C GLU* 1.3 108.7 + - - +
120C PRO* 3.4 3.9 - - - +
134C LEU 3.2 18.1 + - - +
136C GLN* 5.3 3.6 - - - +
148C THR 5.4 1.1 - - - +
149C VAL* 6.4 0.2 - - - +
151C ASP* 5.3 1.8 + - - -
156C ARG* 3.3 9.6 - - - +
371C ARG* 5.0 0.8 - - - +
406C TYR* 3.6 18.2 - - - -
425C GLU* 2.7 40.3 + - - -
427C ILE* 3.8 20.4 - - - +
439C THR* 4.0 32.9 - - + +
440C SER 4.6 4.9 - - - -
441C GLY* 5.1 0.9 - - - +
802C G39 3.4 29.1 + - - +
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Residues in contact with GLU 119 (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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118C ARG* 1.3 103.1 + - - +
120C PRO* 1.3 65.0 - - - +
121C PHE* 3.9 10.2 + - - -
133C PHE* 3.6 10.7 - - - -
134C LEU* 3.7 25.1 + - + +
151C ASP* 4.6 0.7 - - - +
156C ARG* 2.7 33.5 + - - -
227C GLU* 4.3 24.1 - - + +
406C TYR* 4.4 22.0 - - + -
425C GLU* 2.8 15.5 + - - -
802C G39 3.1 29.6 + - - +
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Residues in contact with PRO 120 (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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117C ILE* 4.1 13.9 - - + -
118C ARG* 3.5 3.4 - - - -
119C GLU* 1.3 91.1 - - - +
121C PHE* 1.3 59.6 + - - +
131C THR* 4.7 8.3 - - + -
132C PHE 3.2 11.4 - - - +
133C PHE* 3.9 12.8 - - + -
423C TRP* 3.0 27.1 - - + -
425C GLU* 3.1 39.7 - - + +
441C GLY 5.9 0.9 - - - -
442C SER 4.9 2.0 - - - +
443C SER* 4.5 16.8 - - - -
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Residues in contact with PHE 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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119C GLU 4.1 9.9 - - - -
120C PRO* 1.3 75.6 - - - +
122C ILE* 1.3 69.6 + - - +
123C SER* 4.4 1.6 - - - -
131C THR* 3.4 3.5 - - - +
132C PHE* 2.6 80.1 + + + +
134C LEU* 6.2 0.9 - - + -
158C LEU* 4.4 12.8 - - + -
180C ALA* 4.7 2.5 - - + -
181C SER* 3.9 13.7 - - - -
182C ALA* 3.9 29.4 - - + -
227C GLU* 3.7 16.8 - - - +
228C SER* 3.4 13.9 - - - -
229C GLU* 3.5 22.7 - - - -
423C TRP* 3.4 27.1 - - + +
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Residues in contact with ILE 122 (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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100C TYR* 5.2 0.4 - - + -
101C SER* 4.5 2.7 - - - +
121C PHE* 1.3 81.1 - - - +
123C SER* 1.3 71.7 + - - +
124C CYS* 4.6 4.3 - - - -
129C CYS* 4.7 0.4 - - + -
130C ARG 3.4 11.4 - - - +
131C THR* 4.1 12.8 - - + +
163C VAL* 3.8 20.6 - - + -
229C GLU* 3.8 8.1 + - - +
410C PHE* 3.1 55.6 - - + +
423C TRP* 3.3 19.1 + - + -
443C SER* 5.7 6.1 - - - +
444C ILE 5.5 0.4 - - - -
445C SER* 3.3 36.8 - - - +
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Residues in contact with SER 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 PHE* 4.3 1.5 + - - -
122C ILE* 1.3 77.7 - - - +
124C CYS* 1.3 67.1 + - - +
130C ARG* 2.9 28.3 + - - +
132C PHE* 3.9 21.9 - - - -
182C ALA 3.6 7.3 + - - -
183C CYS* 3.7 4.7 - - - -
189C TRP* 3.4 22.5 - - - -
229C GLU* 3.0 31.8 + - - +
410C PHE* 4.7 0.9 - - - -
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Residues in contact with CYS 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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85C LEU* 5.2 4.0 - - - +
122C ILE* 4.6 0.2 - - - -
123C SER* 1.3 81.2 + - - +
125C SER* 1.3 61.4 + - - +
128C GLU 3.3 5.8 - - - +
129C CYS* 2.1 48.7 - - - -
184C HIS* 3.8 14.2 + - - +
189C TRP* 3.8 5.8 - - - -
229C GLU* 4.0 3.7 + - - +
410C PHE* 4.1 15.9 - - - -
411C VAL 3.8 22.2 + - - +
412C HIS* 3.7 18.1 - - - +
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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