Contacts of the strand formed by residues 206 - 211 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I PRO* 3.0 25.5 - - + +
36I HIS* 3.1 15.1 - - - -
37I GLN* 4.3 0.2 - - - -
196J CYS* 3.6 43.5 - - + +
199J MET* 4.3 11.9 - - + -
200J GLU* 2.9 34.5 + - + +
205J VAL* 1.3 73.4 - - - +
207J GLU* 1.3 64.3 + - - +
208J ALA 3.6 14.1 - - - +
221J VAL* 3.9 6.5 - - + -
222J ALA 3.6 9.0 - - - +
223J THR* 4.3 7.6 - - + -
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Residues in contact with GLU 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ILE* 3.3 10.4 - - - +
34I PRO* 3.1 14.8 - - - +
37I GLN* 3.5 27.9 + - - +
47I LYS* 5.8 0.3 - - - -
205J VAL* 3.7 2.0 + - + -
206J VAL* 1.3 76.3 - - - +
208J ALA* 1.3 66.8 + - + +
222J ALA* 2.8 15.5 + - + +
223J THR 4.1 1.4 - - - +
224J ARG* 3.5 45.1 - - + +
225J PHE* 5.1 0.9 - - - -
4480J ADP 3.5 37.6 + - - +
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Residues in contact with ALA 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I VAL* 5.1 3.8 - - + -
32I THR 3.2 6.1 - - - +
33I ILE* 3.1 24.7 - - + -
34I PRO* 4.0 5.2 - - - -
206J VAL* 3.5 8.5 - - - +
207J GLU* 1.3 85.0 - - + +
209J HIS* 1.3 61.4 - - - +
210J HIS* 5.2 3.5 - - + -
221J VAL* 3.5 1.6 - - - +
222J ALA* 2.6 44.9 + - + +
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Residues in contact with HIS 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I PHE* 4.6 5.4 - + - -
31I VAL* 3.8 1.3 - - - +
32I THR* 2.9 49.0 + - + +
189J GLN* 2.7 36.3 + - - -
192J ARG* 2.7 30.5 + - + +
193J SER* 3.0 30.6 + - - -
196J CYS* 3.6 30.1 - - - -
208J ALA* 1.3 74.4 - - - +
210J HIS* 1.3 67.5 + - - +
220J GLU 3.6 13.7 - - - +
221J VAL* 3.9 7.6 - - + -
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Residues in contact with HIS 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I HIS* 4.8 1.6 - - - +
31I VAL* 4.0 17.3 - - + +
179J TYR* 4.2 11.2 - + - -
180J PHE* 3.4 26.6 - + + -
192J ARG* 3.5 17.9 - - - +
208J ALA* 5.2 3.8 - - + -
209J HIS* 1.3 84.9 + - - +
211J HIS* 1.3 88.3 + - - +
212J GLU* 3.4 24.9 - - - -
220J GLU* 3.2 56.6 + - + +
222J ALA* 5.7 4.2 - - + +
469J MN 4.1 5.3 + - - -
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Residues in contact with HIS 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I HIS* 5.8 1.8 - - + -
155J GLU* 2.7 37.1 + - - -
173J PRO* 4.6 6.1 - - + +
178J GLY* 2.9 21.4 - - - +
179J TYR* 4.8 0.2 - - - -
180J PHE* 4.0 19.9 - - - +
181J PRO 5.8 0.4 - - - -
186J ASP* 3.3 30.0 + - + +
192J ARG* 3.6 11.5 - - - +
210J HIS* 1.3 106.0 + - - +
212J GLU* 1.3 87.3 + - - +
214J ALA 3.6 12.5 + - - -
217J GLY* 4.0 5.6 - - - -
218J GLN 3.1 13.0 + - - -
219J 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