Contacts of the strand formed by residues 115 - 124 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105E SER* 5.8 0.2 - - - -
113E ASP 4.2 0.2 + - - -
114E VAL* 1.3 82.1 - - - +
116E VAL* 1.3 61.6 + - - +
117E ILE* 3.5 23.9 + - + +
133E PHE* 4.3 3.4 - + - -
135E THR* 3.7 24.9 - - + -
137E GLY* 5.5 1.6 - - - -
138E ALA 3.5 16.8 - - - -
139E LEU* 3.8 10.2 - - + +
140E LEU* 4.3 3.9 - - - +
159E MET* 3.7 29.2 - - + -
167E PRO* 2.9 14.7 + - + +
168E SER* 3.3 24.7 - - - -
169E PRO* 3.3 35.4 - - + -
171E SER* 4.0 6.7 - - - -
440E SER* 4.1 2.6 + - - -
108H ILE* 3.6 27.8 - - + -
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Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E VAL 3.6 1.6 + - - -
115E PHE* 1.3 73.2 - - - +
117E ILE* 1.3 66.5 + - - +
135E THR* 3.4 1.7 - - - -
136E GLN* 3.2 44.3 + - + -
138E ALA* 2.8 35.7 + - + +
139E LEU* 4.0 2.5 - - - +
140E LEU* 4.3 16.6 - - + +
145E SER* 4.7 7.2 - - - +
148E THR* 3.9 14.1 - - + +
438E TRP* 5.4 0.4 - - + -
439E THR 3.3 24.5 - - - +
440E SER* 3.5 8.7 - - - -
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Residues in contact with ILE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ASP* 6.1 0.9 - - - +
105E SER* 5.4 0.4 - - - +
115E PHE* 3.5 24.5 - - + +
116E VAL* 1.3 82.9 - - - +
118E ARG* 1.3 69.4 + - - +
120E PRO* 4.1 17.0 - - + -
133E PHE* 3.9 38.6 - - + -
134E LEU 3.4 12.1 - - - +
135E THR* 4.0 4.5 - - - +
136E GLN* 4.8 1.5 - - - +
156E ARG* 4.3 1.6 - - - -
167E PRO* 4.4 14.4 - - + -
439E THR 3.8 2.1 - - - +
440E SER* 2.7 37.1 + - - +
441E GLY* 3.4 29.3 + - - +
442E SER* 5.6 0.9 - - - -
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Residues in contact with ARG 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ILE* 1.3 86.3 - - - +
119E GLU* 1.3 109.5 + - - +
120E PRO* 3.4 4.3 - - - +
134E LEU 3.2 21.0 + - - +
136E GLN* 5.1 3.8 - - - +
148E THR 5.3 1.8 - - - +
151E ASP* 5.2 2.2 + - - -
156E ARG* 3.2 12.6 - - - +
371E ARG* 4.9 0.6 - - - +
406E TYR* 3.6 19.0 - - - -
425E GLU* 2.7 36.8 + - - -
427E ILE* 3.9 21.9 - - - +
439E THR* 4.2 30.3 - - + +
440E SER 4.5 6.3 - - - -
441E GLY 5.0 0.7 - - - +
804E G39 3.5 27.9 + - - +
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Residues in contact with GLU 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E ARG* 1.3 116.8 + - - +
120E PRO* 1.3 66.4 - - - +
121E PHE* 3.9 12.5 - - - -
133E PHE* 3.9 6.9 - - - -
134E LEU* 3.7 19.7 + - + +
151E ASP* 4.5 0.9 - - - +
156E ARG* 3.1 18.5 + - - -
227E GLU* 3.8 34.2 - - + +
406E TYR* 4.3 19.7 - - + -
425E GLU* 2.9 14.3 + - - -
804E G39 2.9 27.6 + - - +
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Residues in contact with PRO 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ILE* 4.1 22.0 - - + -
118E ARG* 3.5 3.4 - - - -
119E GLU* 1.3 92.9 - - - +
121E PHE* 1.3 67.1 + - - +
131E THR* 4.7 9.2 - - + -
132E PHE 3.3 11.9 - - - +
133E PHE* 4.1 3.8 - - + -
227E GLU 4.0 0.3 - - - +
423E TRP* 3.2 21.5 - - + -
425E GLU* 3.1 38.1 - - + +
441E GLY* 6.0 0.2 - - - -
442E SER 4.4 8.1 - - - +
443E SER* 4.7 11.0 - - - -
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Residues in contact with PHE 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E GLU 3.9 8.3 - - - -
120E PRO* 1.3 79.7 - - - +
122E ILE* 1.3 70.0 + - - +
123E SER* 4.5 0.2 - - - -
130E ARG 4.0 0.2 - - - +
131E THR* 4.5 2.3 - - - +
132E PHE* 2.8 71.0 + + + +
134E LEU* 6.2 0.9 - - + -
158E LEU* 4.5 10.5 - - + -
180E ALA* 4.4 9.0 - - + -
181E SER* 4.0 7.4 - - - -
182E ALA* 3.7 23.1 - - + -
227E GLU* 3.6 21.5 - - - +
228E SER* 3.5 4.5 - - - -
229E GLU* 3.3 32.3 - - + -
423E TRP* 3.4 27.1 - - + +
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Residues in contact with ILE 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E TYR* 5.3 0.7 - - + -
101E SER* 4.4 3.4 - - - +
121E PHE* 1.3 78.0 - - - +
123E SER* 1.3 69.5 + - - +
129E CYS* 4.4 5.2 - - + -
130E ARG 3.3 12.8 - - - +
131E THR* 4.0 15.7 - - + +
163E VAL* 3.4 24.0 - - + -
229E GLU* 3.7 6.4 + - - +
410E PHE* 3.0 51.5 - - + +
423E TRP* 3.5 21.7 + - + -
443E SER* 5.7 6.3 - - - +
444E ILE 5.2 0.7 - - - +
445E SER* 3.4 36.6 - - - +
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Residues in contact with SER 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E PHE* 4.2 1.8 + - - -
122E ILE* 1.3 78.0 - - - +
124E CYS* 1.3 67.0 + - - +
130E ARG 3.1 24.6 + - - +
132E PHE* 4.0 10.3 - - - -
182E ALA 3.5 10.8 + - - -
183E CYS* 3.7 12.0 - - - +
189E TRP* 3.3 18.7 - - - -
229E GLU* 2.5 38.3 + - - +
410E PHE* 4.6 1.3 - - - -
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Residues in contact with CYS 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E LEU* 5.3 3.8 - - - +
122E ILE* 4.6 0.2 - - - -
123E SER* 1.3 79.6 + - - +
125E SER* 1.3 67.2 + - - +
128E GLU 3.4 5.6 - - - +
129E CYS* 2.1 47.6 - - - -
184E HIS* 3.6 17.8 + - - +
189E TRP* 3.8 5.8 - - - -
229E GLU* 3.8 3.9 + - - +
410E PHE* 4.0 16.4 - - - -
411E VAL 3.9 21.7 + - - +
412E HIS* 4.0 13.7 - - - +
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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