Contacts of the strand formed by residues 201 - 207 (chain E) in PDB entry 1I43
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 VAL 201 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E HIS* 4.0 13.0 - - + +
157E VAL* 3.3 37.2 - - + -
195E ALA 3.7 22.0 - - - +
196E LEU* 3.8 29.0 + - + +
199E LYS 3.4 1.8 + - - +
200E LYS* 1.3 77.9 - - - +
202E ASN* 1.3 64.2 + - - +
203E LEU 3.6 16.8 - - - +
204E PHE* 4.3 2.9 - - + +
229E LYS 4.7 4.2 + - - +
230E GLY 4.5 2.3 - - - +
231E ALA* 3.4 31.8 + - + +
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Residues in contact with ASN 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E LEU 5.3 2.6 + - - +
150E VAL* 4.7 7.2 - - + -
151E PRO* 3.7 31.1 - - + +
154E GLY* 3.2 12.0 - - - -
155E HIS 2.9 35.6 + - - +
200E LYS* 3.4 18.2 + - - +
201E VAL* 1.3 75.6 - - - +
203E LEU* 1.3 66.1 + - + +
230E GLY 4.5 2.2 - - - +
231E ALA* 3.7 2.3 - - - +
232E LEU* 3.1 22.5 + - - +
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Residues in contact with LEU 203 (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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145E MET* 3.9 26.9 - - + -
149E LEU* 4.4 18.6 - - + -
150E VAL* 4.1 12.8 - - + -
155E HIS 3.8 1.2 + - - -
156E ILE* 3.2 38.5 - - + +
157E VAL 3.2 21.1 + - - -
201E VAL* 3.6 6.2 - - - +
202E ASN* 1.3 84.7 - - - +
204E PHE* 1.3 63.7 + - - +
205E PHE* 3.9 14.8 - - + -
232E LEU* 3.1 30.1 - - + +
233E VAL 4.8 0.2 - - - +
234E CYS* 4.2 16.6 - - + -
254E LEU* 4.9 1.8 - - + -
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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
----------------------------------------------------------
157E VAL* 3.1 46.2 - - + -
158E THR* 4.2 8.3 - - - -
159E THR* 4.3 7.4 - - + -
184E ILE* 4.5 7.0 - - + -
192E LEU* 3.7 18.6 - - + -
201E VAL* 4.3 3.3 - - + +
203E LEU* 1.3 71.9 - - - +
205E PHE* 1.3 64.9 + - - +
206E THR* 3.4 33.0 - - + -
217E VAL* 4.6 5.4 - - + -
222E VAL* 3.3 41.1 - - + -
226E CYS* 3.7 15.9 - - - -
232E LEU 2.5 14.3 + - - +
233E VAL* 3.4 9.4 - - + -
234E CYS 3.0 24.6 + - - +
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Residues in contact with PHE 205 (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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142E SER* 4.7 9.0 - - - -
145E MET* 4.5 11.2 - - + -
146E LEU* 5.2 5.4 - - + -
156E ILE* 4.7 2.9 - - + -
157E VAL 2.8 9.2 + - - +
158E THR* 2.9 45.0 - - + +
162E CYS* 4.0 13.5 - - - -
166E THR* 3.9 28.9 - - + -
170E ILE* 4.9 3.1 - - + -
203E LEU* 3.9 17.8 + - + -
204E PHE* 1.3 75.1 - - - +
206E THR* 1.3 76.0 + - - +
207E GLU* 4.5 6.3 - - - -
234E CYS* 3.6 23.6 - - + -
236E ASP* 4.5 19.7 - - + -
256E LEU* 3.8 29.2 - - + -
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Residues in contact with THR 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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158E THR* 5.5 0.2 - - - -
159E THR* 3.0 32.9 + - - +
162E CYS* 5.7 2.2 - - - -
204E PHE* 3.4 31.0 - - + -
205E PHE* 1.3 85.9 - - - +
207E GLU* 1.3 75.9 + - - +
208E SER* 5.7 0.2 - - - -
210E THR* 4.9 0.5 + - - -
217E VAL* 4.3 13.5 - - + +
234E CYS 3.1 4.7 + - - +
235E ILE* 3.0 26.6 - - + +
236E ASP* 2.9 20.5 + - - -
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Residues in contact with GLU 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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159E THR* 5.7 0.7 - - - +
161E ASP 3.5 10.4 - - - +
162E CYS* 4.2 10.7 - - - -
163E TYR* 3.4 32.3 + - - +
166E THR* 5.9 0.2 - - - -
205E PHE* 4.5 6.4 - - - -
206E THR* 1.3 85.8 + - - +
208E SER* 1.3 65.3 + - - +
209E PRO 3.6 9.3 - - - +
210E THR* 3.7 22.7 + - - +
211E ASN* 3.7 12.0 + - - +
215E ARG 4.3 2.1 - - - +
217E VAL* 4.6 3.5 - - - +
236E ASP* 3.3 36.8 - - + +
239E PHE* 5.8 0.2 - - + -
500E PLP 3.7 20.1 + - + +
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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