Contacts of the strand formed by residues 201 - 207 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F HIS* 4.0 14.8 - - + +
157F VAL* 3.4 37.0 - - + -
195F ALA 3.5 23.1 - - - +
196F LEU* 3.9 29.1 + - + +
199F LYS 3.3 1.6 + - - -
200F LYS* 1.3 77.7 - - - +
202F ASN* 1.3 64.7 + - - +
203F LEU 3.6 20.9 - - - +
204F PHE* 4.4 2.0 - - + +
229F LYS 4.9 3.3 - - - +
230F GLY 4.6 2.4 - - - +
231F ALA* 3.7 25.2 + - + +
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Residues in contact with ASN 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F LEU 5.6 0.9 - - - +
150F VAL* 4.6 8.5 - - + -
151F PRO* 3.8 29.1 - - + +
154F GLY* 3.0 13.7 - - - -
155F HIS 2.8 38.3 + - - +
200F LYS* 3.4 18.6 + - - +
201F VAL* 1.3 76.4 + - - +
203F LEU* 1.3 64.0 + - + +
230F GLY 4.6 2.2 - - - +
231F ALA* 3.9 1.9 - - - -
232F LEU* 3.1 23.7 + - - +
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Residues in contact with LEU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F MET* 3.8 25.8 - - + -
146F LEU* 4.1 1.1 - - + -
149F LEU* 4.5 15.5 - - + -
150F VAL* 4.1 11.0 - - + -
155F HIS 3.8 1.0 + - - -
156F ILE* 3.3 39.4 - - + +
157F VAL 3.1 22.3 + - - -
201F VAL* 3.6 6.7 - - - +
202F ASN* 1.3 84.5 - - - +
204F PHE* 1.3 62.3 + - - +
205F PHE* 4.0 10.1 - - + -
232F LEU* 3.1 30.1 - - + +
233F VAL 4.7 0.4 - - - -
234F CYS* 3.9 23.8 - - + -
254F LEU* 5.0 1.6 - - + -
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Residues in contact with PHE 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F VAL* 3.0 47.8 - - + -
158F THR* 4.1 14.4 - - - -
159F THR* 4.3 8.3 - - + -
184F ILE* 4.6 7.9 - - + -
186F PRO 6.2 0.2 - - - -
192F LEU* 3.8 14.1 - - + -
201F VAL* 4.4 4.0 - - + +
203F LEU* 1.3 72.5 - - - +
205F PHE* 1.3 61.6 + - - +
206F THR* 3.4 29.2 - - + -
217F VAL* 4.6 5.4 - - + -
222F VAL* 3.3 43.7 - - + -
226F CYS* 3.9 18.2 - - - -
231F ALA* 5.4 0.2 - - + -
232F LEU 2.5 13.6 + - - +
233F VAL* 3.5 7.1 - - + -
234F CYS 3.0 25.3 + - - +
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Residues in contact with PHE 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F SER* 4.7 9.0 - - - -
145F MET* 4.3 9.6 - - + -
146F LEU* 5.1 6.5 - - + -
156F ILE* 4.6 3.6 - - + -
157F VAL 2.8 9.3 + - - -
158F THR* 3.0 44.9 - - + +
162F CYS* 4.0 14.4 - - - -
166F THR* 4.0 28.0 - - + -
170F ILE* 5.0 2.9 - - + -
203F LEU* 3.9 17.6 + - + -
204F PHE* 1.3 74.6 - - - +
206F THR* 1.3 70.6 + - - +
207F GLU* 4.3 7.0 - - - -
234F CYS* 3.5 27.1 - - + -
236F ASP* 4.4 21.8 - - + -
256F LEU* 3.7 30.5 - - + -
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Residues in contact with THR 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F THR* 3.2 31.4 + - + +
162F CYS* 5.9 1.8 - - - +
204F PHE* 3.4 33.2 - - + -
205F PHE* 1.3 84.0 - - - +
207F GLU* 1.3 80.1 + - - +
210F THR* 5.1 0.2 + - - -
217F VAL* 4.0 11.7 - - + +
234F CYS 3.1 3.7 + - - +
235F ILE* 3.1 28.9 - - + -
236F ASP* 2.9 22.4 + - - -
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Residues in contact with GLU 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F THR* 5.5 0.9 + - - +
161F ASP 3.6 7.8 - - - +
162F CYS* 3.9 17.0 - - - -
163F TYR* 3.1 32.7 + - - +
166F THR* 5.5 0.2 + - - -
205F PHE* 4.3 6.9 - - - -
206F THR* 1.3 88.4 + - - +
208F SER* 1.3 64.6 + - - +
209F PRO 3.5 5.5 - - - +
210F THR* 3.6 28.0 + - - +
211F ASN* 4.0 8.1 + - - +
215F ARG 4.2 2.4 - - - +
217F VAL* 4.4 3.3 - - - +
235F ILE* 4.6 0.4 - - - -
236F ASP* 3.3 34.7 - - + +
239F PHE* 5.8 0.2 - - + -
500F PLP 3.6 21.8 - - + +
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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