Contacts of the strand formed by residues 209 - 216 (chain E) in PDB entry 1AO7
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 209 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E TRP 3.8 1.7 + - - +
163E VAL* 3.4 3.1 - - - +
164E ASN* 3.0 39.1 + - - +
165E GLY 5.7 1.2 + - - -
208E ASN* 1.3 74.3 - - - +
210E PHE* 1.3 77.7 + - - +
211E ARG* 3.9 31.2 - - + -
240E GLU* 2.7 42.3 + - + +
241E ALA 3.6 11.2 - - - -
242E TRP* 3.6 38.5 - + + -
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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
----------------------------------------------------------
129E VAL* 5.4 3.2 - - + +
145E LEU* 4.2 12.1 - - + -
161E TRP* 4.6 16.8 - - + -
162E TRP 4.0 2.2 - - - -
163E VAL* 3.1 25.4 - - + +
196E LEU* 4.4 13.0 - - + -
198E VAL* 5.2 5.4 - - + -
202E PHE* 3.4 37.5 - + - -
203E TRP* 3.0 50.7 - + + -
208E ASN* 3.9 25.1 - - + -
209E HIS* 1.3 79.8 - - - +
211E ARG* 1.3 61.5 + - - +
240E GLU* 3.3 21.8 - - - -
241E ALA* 3.1 19.2 + - + +
243E GLY* 4.4 0.2 - - - -
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Residues in contact with ARG 211 (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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160E SER 3.7 0.5 - - - +
161E TRP* 3.4 8.5 - - - -
162E TRP* 2.8 70.6 + - - +
165E GLY* 5.3 6.7 - - - +
209E HIS* 3.9 20.6 - - + -
210E PHE* 1.3 75.5 - - - +
212E CYS* 1.3 60.3 + - - +
213E GLN* 2.9 32.5 + - - +
238E SER* 3.6 27.5 + - - -
239E ALA 3.1 20.9 - - - +
240E GLU* 4.4 5.2 - - + +
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Residues in contact with CYS 212 (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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127E VAL* 3.7 5.7 - - + +
129E VAL* 3.7 18.1 - - + +
147E CYS* 2.0 51.6 - - + -
159E LEU* 3.5 24.0 - - - -
160E SER 3.5 3.1 - - - -
161E TRP* 4.2 13.0 - - + -
211E ARG* 1.3 70.9 - - - +
213E GLN* 1.3 59.8 + - - +
214E VAL* 5.0 1.1 - - - -
238E SER* 3.2 5.6 - - - -
239E ALA 2.9 28.3 + - - -
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Residues in contact with GLN 213 (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 GLU 4.5 1.1 - - - +
159E LEU* 3.3 4.9 - - - +
160E SER* 2.8 39.6 + - - +
162E TRP* 2.7 51.0 + - + +
211E ARG* 2.9 22.6 + - - +
212E CYS* 1.3 74.1 - - - +
214E VAL* 1.3 69.4 + - - +
215E GLN* 4.3 2.8 + - + +
236E ILE* 3.8 26.4 - - + +
238E SER* 3.7 17.7 - - - +
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Residues in contact with VAL 214 (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 PRO* 3.7 27.6 - - + -
127E VAL* 3.7 22.7 - - + -
147E CYS* 5.4 0.2 - - - -
149E ALA* 4.1 15.0 - - + -
157E VAL* 4.2 22.0 - - + -
158E GLU 3.6 2.9 - - - +
159E LEU* 3.8 21.3 - - + -
212E CYS* 5.0 0.7 - - - -
213E GLN* 1.3 82.7 - - - +
215E GLN* 1.3 63.6 + - - +
216E PHE* 3.6 1.6 + - - +
236E ILE* 3.4 4.3 - - - -
237E VAL* 3.0 39.9 + - - +
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Residues in contact with GLN 215 (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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156E HIS 3.8 0.3 - - - +
157E VAL* 3.3 7.4 - - - -
158E GLU* 2.8 49.5 + - + +
213E GLN* 4.3 3.3 + - + +
214E VAL* 1.3 71.9 - - - +
216E PHE* 1.3 68.2 + - - +
217E TYR* 3.4 34.4 + - + +
234E THR* 4.9 3.8 - - - -
235E GLN* 2.8 29.4 + - - +
236E ILE* 3.5 22.1 - - + +
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Residues in contact with PHE 216 (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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122E VAL* 4.0 8.7 - - + -
123E PHE 3.9 10.8 - - - -
124E PRO* 3.7 24.5 - - + -
125E PRO* 3.8 27.6 - - + -
152E PHE* 4.5 0.9 - - + -
153E TYR 3.3 28.5 - - - -
154E PRO 3.9 14.8 - - - -
156E HIS 3.7 7.9 - - - -
157E VAL* 4.1 6.7 - - + -
214E VAL 3.6 1.9 + - - +
215E GLN* 1.3 78.4 + - - +
217E TYR* 1.3 82.0 - - - +
218E GLY* 3.8 14.8 - - - -
232E PRO 3.9 10.8 - - - -
233E VAL 3.9 13.0 - - - -
234E THR* 3.3 8.1 - - - -
235E GLN* 2.7 39.4 + - + +
237E VAL* 5.6 0.9 - - + -
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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