Contacts of the strand formed by residues 201 - 207 (chain L) in PDB entry 1I43
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 201 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155L HIS* 3.9 14.1 - - + +
157L VAL* 3.6 36.1 - - + -
195L ALA 3.6 22.7 - - - +
196L LEU* 3.7 29.1 + - + +
199L LYS 3.3 2.0 + - - +
200L LYS* 1.3 76.9 - - - +
202L ASN* 1.3 63.3 + - - +
203L LEU 3.6 21.1 - - - +
204L PHE* 4.4 2.5 - - + +
229L LYS 4.8 3.9 + - - +
230L GLY 4.6 2.6 - - - +
231L ALA* 3.7 25.0 + - + +
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Residues in contact with ASN 202 (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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149L LEU 5.4 0.8 + - - +
150L VAL* 4.6 9.4 - - + -
151L PRO* 3.6 31.9 - - + +
154L GLY* 3.0 31.7 - - - -
155L HIS 2.7 22.4 + - - +
200L LYS* 3.4 16.6 + - - +
201L VAL* 1.3 75.2 + - - +
203L LEU* 1.3 62.2 + - + +
230L GLY 4.6 2.1 - - - +
231L ALA* 3.9 2.1 - - - -
232L LEU* 3.2 21.1 + - - +
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Residues in contact with LEU 203 (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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145L MET* 3.8 32.3 - - + -
146L LEU* 4.0 1.3 - - + -
149L LEU* 4.5 15.7 - - + -
150L VAL* 4.1 11.2 - - + -
155L HIS 3.7 1.6 + - - -
156L ILE* 3.2 37.0 - - + +
157L VAL 3.1 21.7 + - - -
201L VAL* 3.6 6.7 - - - +
202L ASN* 1.3 82.9 - - - +
204L PHE* 1.3 63.3 + - - +
205L PHE* 4.0 10.1 - - + -
232L LEU* 3.2 29.6 - - + +
233L VAL 4.8 0.4 - - - +
234L CYS* 4.1 16.8 - - + -
254L LEU* 4.9 1.6 - - + -
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Residues in contact with PHE 204 (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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157L VAL* 3.0 49.4 - - + -
158L THR* 4.0 9.9 - - - -
159L THR* 4.4 7.9 - - + -
184L ILE* 4.6 7.4 - - + -
192L LEU* 4.0 13.5 - - + -
196L LEU* 6.1 0.2 - - + -
201L VAL* 4.4 3.5 - - + +
203L LEU* 1.3 73.0 - - - +
205L PHE* 1.3 66.8 + - - +
206L THR* 3.4 30.3 - - + -
217L VAL* 4.5 4.7 - - + -
222L VAL* 3.3 42.8 - - + -
226L CYS* 3.8 17.9 - - - -
232L LEU 2.5 14.4 + - - +
233L VAL* 3.5 6.4 - - + -
234L CYS 3.0 25.3 + - - +
235L ILE* 5.2 0.7 - - + -
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Residues in contact with PHE 205 (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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142L SER* 4.5 13.5 - - - -
145L MET* 4.5 8.1 - - + -
146L LEU* 5.0 5.8 - - + -
156L ILE* 4.7 2.9 - - + -
157L VAL 2.8 8.9 + - - -
158L THR* 2.9 45.4 - - + +
162L CYS* 4.2 11.4 - - - -
166L THR* 3.9 28.7 - - + -
170L ILE* 4.9 3.6 - - + -
203L LEU* 3.9 17.6 + - + -
204L PHE* 1.3 75.4 - - - +
206L THR* 1.3 75.0 + - - +
207L GLU* 4.6 6.5 - - - -
234L CYS* 3.5 22.9 - - + -
236L ASP* 4.5 20.4 - - + -
256L LEU* 3.7 27.6 - - + -
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Residues in contact with THR 206 (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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158L THR* 5.5 0.2 - - - -
159L THR* 3.3 31.2 + - - +
162L CYS* 6.2 1.6 - - - +
204L PHE* 3.4 31.9 - - + -
205L PHE* 1.3 85.0 - - - +
207L GLU* 1.3 80.2 + - - +
210L THR* 4.9 0.3 + - - -
217L VAL* 4.1 11.3 - - + +
234L CYS 3.0 4.3 + - - +
235L ILE* 3.1 29.1 - - + +
236L ASP* 2.8 22.8 + - - +
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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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159L THR* 5.7 0.7 - - - +
161L ASP 3.6 9.9 - - - +
162L CYS* 4.1 9.9 - - - -
163L TYR* 3.4 32.2 + - - +
205L PHE* 4.6 5.7 - - - -
206L THR* 1.3 91.7 + - - +
208L SER* 1.3 65.5 + - - +
209L PRO 3.5 9.4 - - - +
210L THR* 3.4 25.8 + - - +
211L ASN* 3.6 12.2 + - - +
215L ARG 4.3 1.6 - - - +
217L VAL* 4.6 3.5 - - - +
235L ILE* 4.7 0.4 - - - -
236L ASP* 3.2 34.7 - - + +
239L PHE* 5.9 0.4 - - + -
500L PLP 3.7 19.6 - - + +
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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