Contacts of the strand formed by residues 203 - 210 (chain E) in PDB entry 2IAN
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 HIS 203 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E TRP 3.8 1.0 + - - +
157E VAL* 3.5 6.2 - - - +
158E ASN* 3.0 43.6 + - - +
159E GLY 5.1 2.8 + - - -
202E ASN* 1.3 73.4 - - - +
204E PHE* 1.3 66.0 + - - +
205E ARG* 3.9 41.0 + - + -
234E GLU* 2.8 35.4 + - + +
235E ALA 3.6 7.6 - - - -
236E TRP* 3.4 50.7 - + + -
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Residues in contact with PHE 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E VAL* 5.4 1.1 - - + +
139E LEU* 3.8 20.9 - - + -
155E TRP* 4.8 7.9 - - + -
156E TRP 3.6 3.1 - - - +
157E VAL* 3.7 22.9 - - + -
190E LEU* 3.9 10.3 - - + -
192E VAL* 4.3 15.3 - - + -
196E PHE* 3.6 42.6 - + - -
197E TRP* 3.5 36.6 - + - -
202E ASN* 4.0 23.3 - - + -
203E HIS* 1.3 75.3 - - - +
205E ARG* 1.3 59.3 + - - +
233E ALA 4.0 0.2 - - - +
234E GLU* 2.9 6.2 - - - +
235E ALA 2.6 48.7 + - - +
237E GLY* 4.1 3.4 - - - -
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Residues in contact with ARG 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E SER 4.2 0.2 - - - +
155E TRP* 3.5 9.4 - - - -
156E TRP* 2.8 63.6 + - + +
159E GLY* 4.8 15.0 - - - -
203E HIS* 3.9 27.3 + - + -
204E PHE* 1.3 73.9 - - - +
206E CYS* 1.3 70.3 + - - +
207E GLN* 3.0 31.4 + - + +
232E SER* 4.0 16.8 - - - -
233E ALA 3.5 5.4 - - - +
234E GLU* 4.1 7.0 + - + +
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Residues in contact with CYS 206 (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 VAL* 4.2 2.2 - - - +
123E VAL* 3.5 17.0 - - + -
141E CYS* 2.0 51.1 - - - -
153E LEU* 3.9 21.5 - - - -
154E SER 3.7 3.1 - - - -
155E TRP* 3.7 13.9 - - + -
204E PHE 4.2 0.2 - - - -
205E ARG* 1.3 72.3 - - - +
207E GLN* 1.3 63.6 + - - +
208E VAL* 4.8 2.0 - - - -
231E VAL 4.1 0.2 - - - +
232E SER* 3.2 26.0 - - - -
233E ALA 2.8 11.5 + - - +
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Residues in contact with GLN 207 (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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152E GLU 3.5 2.3 - - - +
153E LEU* 3.4 1.4 - - - -
154E SER* 2.8 53.1 + - - +
156E TRP* 3.5 31.4 - - + +
205E ARG* 3.0 35.3 + - + +
206E CYS* 1.3 75.9 - - - +
208E VAL* 1.3 64.3 + - - +
209E GLN* 5.4 0.9 - - + +
230E ILE* 3.8 34.1 - - + +
232E SER* 3.9 11.2 + - - +
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Residues in contact with VAL 208 (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 PRO* 4.0 18.1 - - + +
121E VAL* 3.6 26.7 - - + -
143E ALA* 4.4 4.3 - - + -
151E VAL* 3.8 32.5 - - + -
152E GLU 3.4 4.7 - - - +
153E LEU* 3.8 26.9 - - + -
206E CYS* 4.8 3.6 - - - -
207E GLN* 1.3 81.5 - - - +
209E GLN* 1.3 64.9 + - - +
210E PHE* 3.6 1.6 + - - +
229E GLN 3.7 0.3 - - - +
230E ILE* 3.4 5.9 - - - -
231E VAL* 3.0 36.1 + - - +
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Residues in contact with GLN 209 (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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150E HIS 3.7 1.0 - - - +
151E VAL* 3.2 6.4 - - - -
152E GLU* 2.8 48.6 + - + +
207E GLN* 4.2 1.0 - - + +
208E VAL* 1.3 70.8 - - - +
210E PHE* 1.3 58.2 + - - +
211E TYR* 3.4 37.9 + - + +
228E THR* 3.4 25.7 - - - +
229E GLN* 3.4 16.4 - - - +
230E ILE* 3.7 26.8 - - + +
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Residues in contact with PHE 210 (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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116E VAL* 4.0 10.5 - - + -
117E PHE 3.0 26.0 - - - -
118E PRO* 4.2 9.2 - - + -
119E PRO* 3.8 29.4 - - + -
146E PHE* 4.1 5.8 - - + -
147E PHE 3.1 21.5 - - - -
148E PRO* 3.9 11.7 - - + -
150E HIS 3.4 12.3 - - - -
151E VAL* 4.5 6.7 - - + +
208E VAL 3.6 1.1 + - - +
209E GLN* 1.3 73.9 - - - +
211E TYR* 1.3 69.7 + - - +
212E GLY* 3.5 19.7 - - - -
226E PRO 3.9 11.0 - - - -
227E VAL 3.7 13.9 - - - -
228E THR* 3.2 7.4 - - - +
229E GLN* 2.9 43.5 + - + +
231E VAL* 5.7 0.2 - - + -
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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