Contacts of the strand formed by residues 206 - 211 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K PRO* 3.2 19.4 - - + +
36K HIS* 3.2 25.3 - - - -
37K GLN* 4.1 0.9 - - - +
196L CYS* 3.7 43.7 - - + +
199L MET* 4.3 10.1 - - + -
200L GLU* 3.0 30.5 + - + +
205L VAL* 1.3 75.6 - - - +
207L GLU* 1.3 62.5 + - - +
208L ALA 3.6 14.1 - - - +
221L VAL* 4.2 10.1 - - + -
222L ALA 3.6 10.5 - - - +
223L THR* 4.3 4.9 - - + +
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Residues in contact with GLU 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K ILE* 3.2 19.9 - - - +
34K PRO* 3.3 6.6 - - - +
37K GLN* 3.5 28.5 + - - +
47K LYS* 5.7 0.7 - - - -
205L VAL* 3.8 1.7 + - + -
206L VAL* 1.3 73.9 - - - +
208L ALA* 1.3 62.2 + - + +
222L ALA* 2.7 21.6 + - + +
223L THR 3.7 1.4 + - - +
224L ARG* 3.5 39.1 - - + +
225L PHE* 5.2 0.3 - - - -
1482L ADP 3.2 41.4 + - - +
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Residues in contact with ALA 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K VAL* 4.7 5.8 - - + -
32K THR 3.3 7.2 - - - +
33K ILE* 3.2 19.7 - - + -
34K PRO* 4.2 3.8 - - - -
47K LYS* 4.7 12.1 - - - +
206L VAL* 3.6 8.3 - - - +
207L GLU* 1.3 81.4 - - + +
209L HIS* 1.3 61.6 + - - +
210L HIS* 5.0 5.4 - - + -
221L VAL* 3.6 1.0 - - - -
222L ALA* 2.7 44.4 + - + +
1482L ADP 5.6 2.5 - - - +
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Residues in contact with HIS 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K PHE* 4.3 4.5 - + - -
31K VAL* 3.8 0.5 - - - +
32K THR* 2.7 56.5 + - + +
34K PRO* 6.6 0.2 - - + -
189L GLN* 3.2 30.1 + - - -
192L ARG* 2.8 37.3 + - + -
193L SER* 2.8 33.2 + - - -
196L CYS* 3.7 28.9 - - - -
208L ALA* 1.3 75.4 - - - +
210L HIS* 1.3 66.2 + - - +
220L GLU 3.4 11.0 - - - +
221L VAL* 4.0 6.5 - - + -
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Residues in contact with HIS 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K HIS* 4.7 1.1 - - - +
31K VAL* 3.9 20.4 - - + +
50K ASP* 5.3 0.2 - - - -
179L TYR* 3.5 11.7 - - - -
180L PHE* 3.5 23.3 - + + -
192L ARG* 3.4 17.7 - - - +
208L ALA* 5.0 6.7 - - + -
209L HIS* 1.3 83.2 + - - +
211L HIS* 1.3 79.7 + - - +
212L GLU* 3.3 26.2 - - - -
220L GLU* 2.9 51.8 + - + +
222L ALA* 5.8 1.1 - - + -
1482L ADP 2.8 25.4 + - - -
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Residues in contact with HIS 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K HIS* 5.6 2.3 + - + -
155L GLU* 2.7 36.2 + - - -
173L PRO* 4.5 5.8 - - + +
178L GLY* 2.9 21.0 + - - +
179L TYR* 3.0 12.2 - - - -
180L PHE* 3.4 9.7 - - + +
186L ASP* 3.5 30.5 + - + +
192L ARG* 3.6 11.7 - - - +
210L HIS* 1.3 89.9 + - - +
212L GLU* 1.3 92.5 + - - +
214L ALA 3.4 17.4 + - - -
217L GLY* 4.2 5.2 - - - -
218L GLN 2.9 14.5 + - - -
219L ASN* 3.5 14.4 + - - +
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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