Contacts of the strand formed by residues 206 - 211 (chain E) in PDB entry 1F1H
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 206 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E CYS* 3.7 44.4 - - + +
199E MET* 4.3 10.1 - - + -
200E GLU* 3.0 30.6 + - + +
205E VAL* 1.3 74.5 - - - +
207E GLU* 1.3 63.4 - - - +
208E ALA 3.6 13.7 - - - +
221E VAL* 4.2 9.9 - - + -
222E ALA 3.6 11.2 - - - +
223E THR* 4.3 4.7 - - + +
34F PRO* 3.2 26.6 - - + +
36F HIS* 3.2 16.8 - - - -
37F GLN* 4.2 0.3 - - - +
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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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205E VAL* 3.8 1.9 + - + -
206E VAL* 1.3 74.3 - - - +
208E ALA* 1.3 61.9 + - + +
222E ALA* 2.7 20.3 + - + +
223E THR 3.7 1.8 - - - +
224E ARG* 3.5 39.4 - - + +
225E PHE* 5.2 0.5 - - - -
1475E ADP 3.2 43.0 + - - +
33F ILE* 3.2 12.1 - - - +
34F PRO* 3.2 16.0 - - - +
37F GLN* 3.5 28.0 + - - +
47F LYS* 5.8 0.2 - - - -
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Residues in contact with ALA 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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206E VAL* 3.6 7.3 - - - +
207E GLU* 1.3 82.4 - - + +
209E HIS* 1.3 62.1 + - - +
210E HIS* 5.0 4.9 - - + -
221E VAL* 3.6 1.4 - - - -
222E ALA* 2.7 44.3 + - + +
1475E ADP 5.6 2.5 - - - +
31F VAL* 4.8 7.9 - - + -
32F THR 3.2 6.7 - - - +
33F ILE* 3.3 20.4 - - + -
34F PRO* 4.1 4.5 - - - -
47F LYS* 4.9 8.5 - - - +
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Residues in contact with HIS 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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189E GLN* 3.2 32.6 + - - -
192E ARG* 2.8 37.0 + - + -
193E SER* 2.8 32.2 + - - -
196E CYS* 3.7 28.3 - - - -
208E ALA* 1.3 76.4 - - - +
210E HIS* 1.3 64.4 + - - +
220E GLU 3.4 12.3 - - - +
221E VAL* 4.0 6.3 - - + -
16F PHE* 4.3 5.2 - + - -
31F VAL* 3.9 0.3 - - - +
32F THR* 2.8 53.6 + - + +
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Residues in contact with HIS 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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179E TYR* 3.5 11.2 - - - -
180E PHE* 3.5 24.3 - + + -
192E ARG* 3.4 16.4 - - - +
208E ALA* 5.0 5.8 - - + -
209E HIS* 1.3 86.3 + - - +
211E HIS* 1.3 78.7 + - - +
212E GLU* 3.3 26.2 - - - -
220E GLU* 2.9 53.3 + - + +
222E ALA* 5.8 1.3 - - + -
469E MN 4.4 0.2 - - - -
1475E ADP 2.8 25.6 + - - -
30F HIS* 4.8 1.1 - - - +
31F VAL* 4.0 18.6 - - + +
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Residues in contact with HIS 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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155E GLU* 2.7 35.8 + - - -
173E PRO* 4.5 6.4 - - + +
178E GLY* 2.9 20.9 + - - +
179E TYR* 3.0 12.2 - - - -
180E PHE* 3.4 10.8 - - + +
186E ASP* 3.5 31.1 + - + +
192E ARG* 3.6 11.3 - - - +
210E HIS* 1.3 90.5 + - - +
212E GLU* 1.3 91.9 + - - +
214E ALA 3.4 17.0 + - - -
217E GLY* 4.2 5.2 - - - -
218E GLN 2.9 14.4 + - - -
219E ASN* 3.5 14.6 + - - +
30F HIS* 5.7 1.4 + - + -
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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