Contacts of the strand formed by residues 201 - 208 (chain H) in PDB entry 6DF3
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 TYR 201 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H LEU* 4.4 15.2 - - + +
169H TYR* 5.3 5.6 - + + -
170H TRP* 3.4 15.5 - - - +
171H ARG* 3.1 51.7 + - + -
193H GLU* 4.1 25.6 - - + +
194H THR 4.4 1.7 + - - -
195H MET* 3.7 45.2 - - + -
196H GLU* 3.2 24.7 + - - +
199H ALA 3.6 10.1 - - - -
200H ALA* 1.3 74.1 - - - +
202H CYS* 1.3 61.7 + - - +
203H VAL* 5.1 2.7 - - - +
222H GLU 4.1 0.3 - - - +
223H CYS* 3.4 1.2 - - - -
224H VAL* 3.0 31.8 + - + +
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Residues in contact with CYS 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H TYR* 3.3 2.1 - - - -
170H TRP* 2.9 49.7 + - + +
172H ARG* 3.8 30.3 - - - -
201H TYR* 1.3 76.1 - - - +
203H VAL* 1.3 69.7 + - - +
221H THR* 3.7 11.0 - - + -
222H GLU 3.3 3.8 - - - +
223H CYS* 2.1 45.5 - - - -
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Residues in contact with VAL 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H MET* 4.2 6.0 - - + +
145H ILE* 3.4 41.3 - - + -
152H LEU* 3.9 14.6 - - + -
154H ILE* 5.4 0.2 - - + -
167H VAL* 5.0 4.0 - - + -
168H ALA 3.5 6.5 - - - +
169H TYR* 3.5 20.0 - - + -
170H TRP* 5.0 1.1 - - - -
192H LEU* 3.9 20.9 - - + -
201H TYR 5.1 2.0 - - - +
202H CYS* 1.3 82.6 - - - +
204H LYS* 1.3 61.5 + - - +
220H GLN 3.9 1.4 - - - +
221H THR* 3.4 4.7 - - - +
222H GLU* 2.8 47.0 + - + +
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Residues in contact with LYS 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H MET* 3.5 9.0 - - - -
167H VAL* 3.6 4.5 - - - +
168H ALA* 3.0 35.1 + - + +
170H TRP* 4.2 14.2 - - + -
178H GLU* 4.0 22.3 + - - -
203H VAL* 1.3 75.4 - - - +
205H ALA* 1.3 59.8 + - - +
218H PHE* 3.4 49.9 - - + +
219H SER* 3.7 19.3 - - - +
220H GLN 4.4 0.2 - - - -
221H THR* 3.9 18.2 - - - +
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Residues in contact with ALA 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H PRO* 3.2 14.1 - - + +
143H MET* 3.4 17.5 - - + -
154H ILE* 4.5 0.9 - - + -
156H LEU* 3.5 28.3 - - + -
166H LEU 3.3 10.1 - - - +
167H VAL* 4.2 9.0 - - + -
204H LYS* 1.3 77.9 - - - +
206H GLU* 1.3 60.9 + - - +
218H PHE* 4.0 2.9 - - - -
219H SER* 2.9 29.0 + - - -
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Residues in contact with GLU 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H PRO* 4.0 4.5 - - - -
165H PHE* 3.4 10.2 - - - +
166H LEU* 2.9 60.6 + - + +
205H ALA* 1.3 75.5 - - - +
207H THR* 1.3 62.7 + - - +
215H TYR* 3.6 24.1 - - - +
216H SER* 3.1 33.5 - - - +
217H ALA 4.1 3.8 - - - +
218H PHE* 3.5 35.1 - - + -
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Residues in contact with THR 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ASN* 5.4 0.2 - - - +
138H LEU* 4.2 11.0 - - + -
139H THR 4.5 6.5 - - - +
141H PRO* 4.3 3.6 - - - +
159H LEU* 3.5 25.1 - - + +
163H PHE* 3.6 26.9 - - + -
164H GLU 3.4 5.5 + - - -
165H PHE* 3.7 12.7 - - - +
166H LEU* 5.4 0.7 - - - -
206H GLU* 1.3 75.0 - - - +
208H PHE* 1.3 60.8 + - - +
215H TYR* 3.1 12.3 - - - +
216H SER* 3.0 49.4 + - - +
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Residues in contact with PHE 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H GLN 3.9 0.5 - - - +
163H PHE* 3.5 3.5 - - - -
164H GLU* 2.6 62.8 + - + +
166H LEU* 5.7 4.7 - - + +
207H THR* 1.3 73.4 - - - +
209H VAL* 1.3 62.3 - - - +
210H LYS* 3.7 38.9 + - + -
213H GLY* 4.0 18.2 - - - -
214H ARG 3.4 18.2 - - - -
215H TYR* 3.2 52.5 - + + -
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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