Contacts of the strand formed by residues 155 - 160 (chain E) in PDB entry 1IB1
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 ARG 155 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99E TRP* 5.1 0.8 - - - -
101E GLU 3.0 18.8 + - - -
102E GLU* 2.8 56.5 + - - +
117E HIS* 3.3 9.6 + - + +
118E SER* 3.3 24.9 + - - +
119E ALA 2.9 21.9 + - - -
153E VAL* 3.5 2.0 - - - +
154E ARG* 1.3 81.2 - - + +
156E ALA* 1.3 74.1 + - - +
157E VAL* 3.3 23.2 - - - +
192E HIS* 4.1 21.0 + - - -
193E CYS 3.1 20.2 - - - +
194E SER* 4.3 3.1 - - - +
195E LEU* 3.5 13.1 - - - +
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Residues in contact with ALA 156 (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 ALA* 3.3 14.4 - - + +
121E LEU* 4.2 4.9 - - + -
144E LEU* 3.9 27.4 - - + -
147E VAL* 5.7 0.4 - - + -
155E ARG* 1.3 74.3 - - - +
157E VAL* 1.3 68.9 + - - +
173E PHE* 3.8 14.7 - - + -
192E HIS* 3.5 0.7 - - - -
193E CYS* 2.8 36.0 + - + +
195E LEU* 4.4 7.6 - - + -
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Residues in contact with VAL 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E TRP* 4.9 2.9 - - + -
102E GLU 4.8 0.2 - - - +
104E LEU* 4.0 23.1 - - + -
118E SER* 4.3 10.5 - - - -
119E ALA 2.9 9.7 + - - +
120E HIS* 3.4 26.6 - - + +
121E LEU* 2.8 29.9 + - - +
155E ARG* 3.3 33.7 - - - +
156E ALA* 1.3 79.1 - - - +
158E LEU* 1.3 62.5 + - - +
173E PHE* 4.5 0.2 - - - -
191E MET 3.4 5.4 - - - +
192E HIS* 3.3 21.8 - - + +
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Residues in contact with LEU 158 (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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104E LEU* 4.4 9.1 - - - +
120E HIS* 4.8 0.4 - - - -
121E LEU* 3.8 35.7 - - + +
124E LEU* 5.7 0.4 - - + -
140E LEU* 5.1 0.2 - - + -
157E VAL* 1.3 76.3 - - - +
159E MET* 1.3 72.1 + - - +
168E TYR* 3.9 40.8 - - + -
173E PHE* 3.6 33.7 - - + -
190E GLU* 3.7 3.3 - - - +
191E MET* 2.8 53.4 + - + +
401E COT 4.7 6.1 - - + -
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Residues in contact with MET 159 (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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104E LEU* 4.7 1.9 - - + +
109E LEU* 3.7 30.7 - - + -
120E HIS* 4.6 9.9 - - - +
121E LEU 4.8 3.4 + - - +
122E HIS* 5.3 4.0 - - - +
158E LEU* 1.3 76.2 - - - +
160E CYS* 1.3 63.7 + - - +
179E CYS* 3.8 29.6 - - - -
181E ILE* 3.8 20.4 - - + -
183E VAL* 5.1 0.9 - - + -
188E PHE* 3.7 33.7 - - + -
189E THR 3.2 11.9 - - - +
190E GLU* 4.7 0.2 - - - -
401E COT 3.0 56.5 + - + +
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Residues in contact with CYS 160 (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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159E MET* 1.3 76.2 - - - +
161E GLU* 1.3 73.9 + - - +
164E LEU* 4.0 2.7 - - + -
165E VAL* 3.9 21.3 - - - -
168E TYR* 3.6 28.7 - - + -
188E PHE* 3.2 10.8 - - - +
189E THR* 2.8 32.1 + - - +
191E MET* 3.9 13.7 - - - -
401E COT 3.5 25.4 - - - -
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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