Contacts of the strand formed by residues 203 - 208 (chain E) in PDB entry 4D9R
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 ILE 203 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E TRP* 3.3 10.3 - - - -
163E ASN* 2.8 54.9 + - + +
201E THR* 3.6 27.1 - - + +
202E TYR* 1.3 75.6 - - - +
204E CYS* 1.3 65.9 + - - +
205E ASN* 3.7 16.1 - - - +
216E ASP* 4.0 9.9 - - + -
217E LYS 3.2 27.4 - - - +
218E LYS* 4.3 8.3 - - + +
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Residues in contact with CYS 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E VAL* 3.9 8.7 - - - -
148E CYS* 2.0 49.8 - - + -
160E VAL* 4.3 7.9 - - + -
161E SER 3.4 6.3 - - - +
162E TRP* 3.7 21.6 - - + -
203E ILE* 1.3 73.3 - - - +
205E ASN* 1.3 59.8 + - - +
206E VAL* 4.0 4.9 - - - -
215E VAL 3.5 1.9 - - - +
216E ASP* 3.4 4.0 - - - -
217E LYS* 3.0 45.5 + - - -
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Residues in contact with ASN 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E THR* 3.4 2.6 + - - +
160E VAL* 3.3 4.7 - - - -
161E SER* 2.8 55.2 + - - +
163E ASN 3.5 2.4 + - - -
164E SER* 2.8 41.4 + - - +
203E ILE* 3.7 16.9 - - - +
204E CYS* 1.3 71.4 - - - +
206E VAL* 1.3 61.3 + - - +
207E ASN* 4.1 1.0 + - - +
215E VAL 3.6 0.2 - - - -
216E ASP* 2.7 32.2 + - - +
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Residues in contact with VAL 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E PRO* 4.4 10.3 - - + -
129E VAL* 3.9 35.9 - - + -
150E VAL* 3.7 38.4 - - + -
158E VAL* 4.7 4.0 - - + -
159E THR 3.4 7.2 - - - +
160E VAL* 4.4 8.7 - - + -
204E CYS* 4.0 14.1 - - - -
205E ASN* 1.3 76.4 - - - +
207E ASN* 1.3 66.6 + - - +
213E THR* 3.8 1.4 - - + +
214E LYS* 3.4 6.0 - - - +
215E VAL* 2.8 43.6 + - + +
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Residues in contact with ASN 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E VAL* 3.2 7.2 - - - -
159E THR* 2.9 51.4 + - - +
205E ASN 4.1 1.1 + - - +
206E VAL* 1.3 73.5 - - - +
208E HIS* 1.3 69.8 + - - +
209E LYS* 3.6 37.0 + - - +
212E ASN* 5.2 1.4 - - - -
213E THR 3.3 10.3 + - - +
214E LYS* 3.7 38.0 - - - +
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Residues in contact with HIS 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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125E LYS 3.2 19.9 + - - -
126E GLY* 3.7 4.3 - - - -
127E PRO* 3.5 23.1 - - + -
153E TYR* 3.7 9.4 - + - -
154E PHE 3.4 9.2 + - - -
155E PRO 2.8 29.4 - - - -
157E PRO 3.2 14.6 + - - -
158E VAL* 3.4 13.1 - - + +
206E VAL* 5.1 0.2 - - - +
207E ASN* 1.3 73.9 + - - +
209E LYS* 1.4 61.4 + - - +
210E PRO* 3.8 16.0 - - + +
211E SER* 2.8 35.0 + - - +
212E ASN 3.1 16.3 + - - -
213E THR 2.8 18.3 + - - +
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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