Contacts of the strand formed by residues 115 - 124 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105F SER* 5.4 0.9 + - - -
113F ASP 4.3 0.4 + - - -
114F VAL* 1.3 83.4 - - - +
116F VAL* 1.3 62.7 + - - +
117F ILE* 3.5 24.3 + - + +
133F PHE* 4.2 6.5 - + - -
135F THR* 3.8 22.4 - - + -
137F GLY* 5.2 1.8 - - - -
138F ALA 3.4 17.7 - - - -
139F LEU* 3.7 10.5 - - + +
140F LEU* 4.4 2.8 - - - +
159F MET* 3.6 32.3 - - + -
167F PRO* 3.0 15.2 + - + +
168F SER* 3.7 20.4 - - - -
169F PRO* 3.6 27.4 - - + -
171F SER* 4.3 1.8 - - - -
440F SER* 4.1 3.5 + - - -
108G ILE* 3.4 37.0 - - + -
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Residues in contact with VAL 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F VAL 3.6 1.6 + - - -
115F PHE* 1.3 71.8 - - - +
117F ILE* 1.3 65.5 + - - +
135F THR* 3.5 1.7 - - - -
136F GLN* 3.3 39.6 + - + +
138F ALA* 3.1 34.5 + - + +
139F LEU 4.2 1.3 - - - +
140F LEU* 4.5 16.4 - - + +
145F SER* 5.1 6.5 - - - +
148F THR* 3.8 22.2 - - + +
438F TRP* 5.4 0.7 - - + -
439F THR 3.2 27.1 - - - +
440F SER* 3.6 10.1 - - - +
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Residues in contact with ILE 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ASP* 6.0 1.8 - - - +
105F SER* 5.2 0.7 - - - +
115F PHE* 3.5 25.3 + - + +
116F VAL* 1.3 82.9 - - - +
118F ARG* 1.3 76.1 + - - +
120F PRO* 4.4 15.7 - - + -
131F THR* 6.3 0.7 - - + -
133F PHE* 3.7 38.4 - - + -
134F LEU 3.4 12.6 - - - +
135F THR* 4.1 2.7 - - - +
136F GLN* 4.9 1.8 - - - -
156F ARG* 4.6 1.3 - - - -
167F PRO* 4.1 18.4 - - + -
439F THR 4.0 1.4 - - - +
440F SER* 3.0 27.5 + - - +
441F GLY 3.4 25.7 + - - +
442F SER* 5.9 0.4 - - - -
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Residues in contact with ARG 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F ILE* 1.3 85.5 - - - +
119F GLU* 1.3 108.3 + - - +
120F PRO* 3.4 6.3 - - - +
134F LEU 3.2 17.3 + - - +
136F GLN* 5.3 0.4 - - - +
148F THR 5.3 4.0 - - - +
151F ASP* 5.5 1.4 + - - -
156F ARG* 3.3 12.3 - - - +
371F ARG* 4.8 0.6 - - - +
406F TYR* 3.6 23.8 - - - -
425F GLU* 2.5 34.0 + - - -
427F ILE* 4.0 22.2 - - - +
439F THR* 4.3 32.4 - - + +
440F SER 4.5 6.5 - - - -
441F GLY* 5.1 0.9 - - - +
805F G39 3.4 28.1 + - - +
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Residues in contact with GLU 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ARG* 1.3 114.9 + - - +
120F PRO* 1.3 66.1 - - - +
121F PHE* 3.9 13.0 - - - -
133F PHE* 3.9 7.4 - - - -
134F LEU* 3.7 27.2 + - + +
151F ASP* 4.8 0.3 - - - +
156F ARG* 3.0 15.2 + - - -
227F GLU* 4.1 25.4 - - + +
406F TYR* 4.4 20.6 - - + -
425F GLU* 2.9 15.1 + - - -
805F G39 3.0 30.7 + - - +
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Residues in contact with PRO 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F ILE* 4.4 20.4 - - + -
118F ARG* 3.4 4.9 - - - -
119F GLU* 1.3 90.7 - - - +
121F PHE* 1.3 66.4 + - - +
131F THR* 4.8 6.7 - - + -
132F PHE 3.4 10.3 - - - +
133F PHE* 4.2 3.1 - - + -
227F GLU 4.2 0.3 - - - +
423F TRP* 3.2 27.0 - - + -
425F GLU* 3.1 41.5 - - + +
441F GLY* 5.8 1.1 - - - -
442F SER 4.6 6.5 - - - +
443F SER* 4.7 14.1 - - - -
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Residues in contact with PHE 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F GLU 3.9 11.9 - - - -
120F PRO* 1.3 76.3 - - - +
122F ILE* 1.3 66.3 + - - +
131F THR* 3.5 2.9 - - - +
132F PHE* 2.7 79.9 + + + +
133F PHE 4.8 0.2 - - - -
134F LEU* 6.2 1.3 - - + -
158F LEU* 4.4 12.8 - - + -
180F ALA* 4.7 3.4 - - + -
181F SER* 4.1 11.2 - - - -
182F ALA* 3.8 28.3 - - + -
227F GLU* 3.8 16.2 - - - +
228F SER* 3.4 17.7 - - - -
229F GLU* 3.4 25.1 - - + -
423F TRP* 3.4 22.2 - - + +
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Residues in contact with ILE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F SER* 4.3 3.8 - - - +
121F PHE* 1.3 78.1 - - - +
123F SER* 1.3 70.7 + - - +
129F CYS* 4.5 3.8 - - + -
130F ARG 3.4 10.3 - - - +
131F THR* 3.6 21.5 - - + +
163F VAL* 3.5 22.4 - - + -
229F GLU* 3.9 7.3 + - - +
410F PHE* 3.2 54.1 - - + +
423F TRP* 3.4 17.3 + - + -
443F SER* 5.7 6.7 - - - +
444F ILE 5.5 0.7 - - - -
445F SER* 3.4 36.8 - - - +
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Residues in contact with SER 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F PHE* 4.2 1.5 + - - -
122F ILE* 1.3 77.0 - - - +
124F CYS* 1.3 65.3 + - - +
130F ARG* 3.0 26.7 + - - +
132F PHE* 4.0 17.4 - - - -
182F ALA 4.1 2.7 - - - -
183F CYS* 3.7 11.8 - - - +
189F TRP* 3.3 24.1 - - - -
229F GLU* 2.9 34.6 + - - -
410F PHE* 4.8 1.1 - - - -
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Residues in contact with CYS 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F LEU* 5.1 4.3 - - - +
122F ILE* 4.6 0.4 - - - -
123F SER* 1.3 79.9 + - - +
125F SER* 1.3 67.1 + - - +
128F GLU 3.3 6.1 - - - +
129F CYS* 2.1 48.2 - - - -
184F HIS* 3.6 16.1 + - - +
189F TRP* 3.8 5.4 - - - -
229F GLU* 3.9 4.1 + - - +
410F PHE* 4.1 15.7 - - - -
411F VAL 4.0 20.4 + - - +
412F HIS* 4.0 13.2 - - - +
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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