Contacts of the strand formed by residues 206 - 211 (chain I) in PDB entry 1FPY
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H PRO* 3.0 29.2 - - + +
36H HIS* 3.1 15.1 - - - -
196I CYS* 3.6 42.4 - - + +
199I MET* 4.3 11.9 - - + -
200I GLU* 2.9 34.5 + - + +
205I VAL* 1.3 72.7 - - - +
207I GLU* 1.3 63.7 + - - +
208I ALA 3.6 13.7 - - - +
221I VAL* 3.9 7.4 - - + -
222I ALA 3.6 9.4 - - - +
223I THR* 4.3 7.6 - - + -
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Residues in contact with GLU 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ILE* 3.4 10.2 - - - +
34H PRO* 3.1 14.7 - - - +
37H GLN* 3.5 27.9 + - - +
47H LYS* 5.8 0.5 - - - -
205I VAL* 3.7 2.0 + - + -
206I VAL* 1.3 75.6 - - - +
208I ALA* 1.3 66.8 + - + +
222I ALA* 2.8 16.2 + - + +
223I THR 4.1 1.2 - - - +
224I ARG* 3.5 45.6 - - + +
225I PHE* 5.1 0.9 - - - -
4479I ADP 3.5 38.2 + - - +
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Residues in contact with ALA 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H VAL* 5.1 3.8 - - + -
32H THR 3.2 6.5 - - - +
33H ILE* 3.1 24.0 - - + -
34H PRO* 4.0 5.6 - - - -
206I VAL* 3.5 8.7 - - - +
207I GLU* 1.3 84.5 - - + +
209I HIS* 1.3 60.7 + - - +
210I HIS* 5.2 3.5 - - + -
221I VAL* 3.5 1.6 - - - +
222I ALA* 2.6 44.6 + - + +
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Residues in contact with HIS 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H PHE* 4.6 5.6 - + - -
31H VAL* 3.8 0.9 - - - +
32H THR* 2.9 48.9 + - + +
189I GLN* 2.7 36.3 + - - -
192I ARG* 2.7 31.3 + - + +
193I SER* 3.0 30.3 + - - -
196I CYS* 3.6 30.7 - - - -
208I ALA* 1.3 74.4 - - - +
210I HIS* 1.3 66.4 + - - +
220I GLU 3.6 13.2 - - - +
221I VAL* 3.9 7.2 - - + -
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Residues in contact with HIS 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H HIS* 4.9 1.3 - - - +
31H VAL* 4.0 15.9 - - + +
32H THR 5.2 0.4 - - - +
179I TYR* 4.2 10.7 - + - -
180I PHE* 3.4 27.9 - + + -
192I ARG* 3.5 18.4 - - - +
208I ALA* 5.2 4.3 - - + -
209I HIS* 1.3 86.5 + - - +
211I HIS* 1.3 87.5 + - - +
212I GLU* 3.4 25.4 - - - -
220I GLU* 3.2 56.7 + - + +
222I ALA* 5.7 4.2 - - + +
469I MN 4.1 5.1 + - - -
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Residues in contact with HIS 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H HIS* 5.8 1.8 + - + -
155I GLU* 2.7 36.5 + - - -
173I PRO* 4.6 5.6 - - + +
178I GLY* 2.9 21.9 - - - +
179I TYR* 4.1 0.6 - - - -
180I PHE* 4.0 20.4 - - - +
181I PRO 5.8 0.2 - - - -
186I ASP* 3.3 30.8 + - + +
192I ARG* 3.6 11.5 - - - +
210I HIS* 1.3 105.6 + - - +
212I GLU* 1.3 86.4 + - - +
214I ALA 3.6 12.3 + - - -
217I GLY* 4.0 6.1 - - - -
218I GLN 3.1 12.6 + - - -
219I ASN* 3.7 15.5 + - - +
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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