Contacts of the strand formed by residues 206 - 211 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A CYS* 3.6 42.8 - - + +
199A MET* 4.3 11.9 - - + -
200A GLU* 2.9 34.7 + - + +
205A VAL* 1.3 74.7 - - - +
207A GLU* 1.3 62.7 + - - +
208A ALA 3.6 13.9 - - - +
221A VAL* 3.9 7.2 - - + -
222A ALA 3.6 8.5 - - - +
223A THR* 4.3 7.4 - - + -
34B PRO* 3.1 25.7 - - + +
36B HIS* 3.1 15.2 - - - -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL* 3.7 1.7 + - + -
206A VAL* 1.3 76.1 - - - +
208A ALA* 1.3 65.1 + - + +
222A ALA* 2.8 16.8 + - + +
223A THR 4.1 1.2 - - - +
224A ARG* 3.5 44.8 - - + +
225A PHE* 5.1 0.9 - - - -
4471A ADP 3.5 37.8 + - - +
33B ILE* 3.4 10.0 - - - +
34B PRO* 3.2 15.2 - - - +
37B GLN* 3.6 25.8 + - - +
47B LYS* 5.8 0.7 - - - -
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL* 3.5 8.9 - - - +
207A GLU* 1.3 84.5 - - + +
209A HIS* 1.4 61.2 + - - +
210A HIS* 5.2 3.9 - - + -
221A VAL* 3.5 1.4 - - - +
222A ALA* 2.6 44.7 + - + +
31B VAL* 5.1 4.3 - - + -
32B THR 3.2 6.7 - - - +
33B ILE* 3.2 23.8 - - + -
34B PRO* 4.1 5.4 - - - -
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Residues in contact with HIS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLN* 2.7 36.0 + - - -
192A ARG* 2.7 32.1 + - + +
193A SER* 3.0 30.4 + - - -
196A CYS* 3.6 31.4 - - - -
208A ALA* 1.4 76.2 - - - +
210A HIS* 1.3 68.2 + - - +
220A GLU 3.6 12.1 - - - +
221A VAL* 3.9 8.3 - - + -
16B PHE* 4.6 5.6 - + - -
31B VAL* 3.8 1.5 - - - +
32B THR* 3.0 47.3 + - + +
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TYR* 4.2 10.5 - + - -
180A PHE* 3.4 27.2 - + + -
192A ARG* 3.5 18.5 - - - +
208A ALA* 5.2 4.7 - - + -
209A HIS* 1.3 86.7 + - - +
211A HIS* 1.3 86.5 + - - +
212A GLU* 3.4 25.6 - - - -
220A GLU* 3.2 56.9 + - + +
222A ALA* 5.7 3.3 - - + +
469A MN 4.1 5.5 + - - -
30B HIS* 4.9 1.6 - - - +
31B VAL* 4.0 15.9 - - + +
32B THR 5.2 0.2 - - - +
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Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLU* 2.7 36.1 + - - -
173A PRO* 4.6 6.1 - - + +
178A GLY* 2.9 22.3 - - - +
179A TYR* 4.1 0.3 - - - -
180A PHE* 4.0 21.2 - - - +
181A PRO 5.8 0.2 - - - -
186A ASP* 3.3 32.1 + - + +
192A ARG* 3.6 10.5 - - - +
210A HIS* 1.3 106.3 + - - +
212A GLU* 1.3 87.3 + - - +
214A ALA 3.6 11.7 + - - -
217A GLY* 4.0 6.5 - - - -
218A GLN 3.1 12.5 + - - -
219A ASN* 3.7 15.3 + - - +
30B HIS* 5.9 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