Contacts of the strand formed by residues 201 - 207 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I HIS* 4.2 13.9 - - + +
157I VAL* 3.4 37.7 - - + -
195I ALA 3.6 22.9 - - - +
196I LEU* 3.7 30.1 + - + +
199I LYS 3.4 1.4 + - - +
200I LYS* 1.3 76.6 - - - +
202I ASN* 1.3 64.1 + - - +
203I LEU 3.7 19.7 - - - +
204I PHE* 4.4 2.7 - - + +
229I LYS 4.8 4.2 + - - +
230I GLY 4.6 2.3 - - - +
231I ALA* 3.7 25.4 + - + +
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Residues in contact with ASN 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I LEU 5.5 1.1 - - - +
150I VAL* 4.5 7.0 - - + -
151I PRO* 3.8 31.0 - - + +
154I GLY* 3.0 13.0 - - - -
155I HIS 2.9 39.1 + - - +
200I LYS* 3.5 17.5 + - - +
201I VAL* 1.3 74.6 - - - +
203I LEU* 1.3 63.1 + - + +
230I GLY 4.6 2.4 - - - +
231I ALA* 3.9 2.1 - - - -
232I LEU* 3.2 23.4 + - - +
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Residues in contact with LEU 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I MET* 3.7 32.3 - - + -
146I LEU* 4.1 1.3 - - + -
149I LEU* 4.3 18.4 - - + -
150I VAL* 4.1 12.1 - - + -
155I HIS 3.7 1.6 + - - -
156I ILE* 3.2 38.2 - - + +
157I VAL 3.1 21.0 + - - -
201I VAL* 3.6 6.4 - - - -
202I ASN* 1.3 84.1 - - - +
204I PHE* 1.3 63.2 + - - +
205I PHE* 4.0 10.3 - - + -
232I LEU* 3.3 28.5 - - + +
234I CYS* 4.3 15.3 - - + -
254I LEU* 5.1 1.3 - - + -
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Residues in contact with PHE 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I VAL* 3.1 38.6 - - + -
158I THR* 4.1 9.2 - - - -
159I THR* 4.4 8.7 - - + -
184I ILE* 4.6 7.4 - - + -
186I PRO 6.1 0.2 - - - -
192I LEU* 3.8 16.8 - - + -
201I VAL* 4.4 3.9 - - + +
203I LEU* 1.3 73.2 - - - +
205I PHE* 1.3 64.7 + - - +
206I THR* 3.5 30.5 - - + -
217I VAL* 4.6 4.9 - - + -
222I VAL* 3.2 43.3 - - + -
226I CYS* 3.7 21.1 - - - -
232I LEU 2.6 11.0 + - - +
233I VAL* 3.6 7.8 - - + -
234I CYS 3.1 25.3 + - - +
235I ILE* 5.1 0.2 - - + -
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Residues in contact with PHE 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I SER* 4.7 9.6 - - - -
145I MET* 4.4 11.4 - - + -
146I LEU* 5.2 5.2 - - + -
156I ILE* 4.6 2.5 - - + -
157I VAL 2.7 9.5 + - - -
158I THR* 3.0 44.9 - - + +
162I CYS* 3.9 22.2 - - - -
166I THR* 4.0 20.0 - - + -
170I ILE* 4.9 3.1 - - + -
203I LEU* 3.8 17.6 + - + -
204I PHE* 1.3 75.1 - - - +
206I THR* 1.3 71.7 + - - +
207I GLU* 4.4 7.6 - - - -
234I CYS* 3.5 22.0 - - + -
236I ASP* 4.4 20.9 - - + -
256I LEU* 3.6 29.8 - - + -
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Residues in contact with THR 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I THR* 3.1 33.5 + - - +
162I CYS* 5.6 2.2 - - - -
204I PHE* 3.5 30.1 - - + -
205I PHE* 1.3 83.6 - - - +
207I GLU* 1.3 76.9 + - - +
210I THR* 5.0 0.3 + - - -
217I VAL* 4.2 13.9 - - + +
234I CYS 3.2 4.3 + - - +
235I ILE* 3.1 27.2 - - + +
236I ASP* 2.9 21.9 + - - -
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Residues in contact with GLU 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159I THR* 5.6 0.2 - - - +
161I ASP 3.5 8.7 - - - +
162I CYS* 4.3 13.2 - - - -
163I TYR* 3.1 35.8 + - - +
166I THR* 5.5 0.3 + - - -
205I PHE* 4.4 5.7 - - - -
206I THR* 1.3 86.6 + - - +
208I SER* 1.3 65.9 + - - +
209I PRO 3.6 10.0 - - - +
210I THR* 3.7 22.6 + - - +
211I ASN* 4.0 8.7 + - - +
215I ARG 4.3 1.9 - - - +
217I VAL* 4.6 3.3 - - - +
236I ASP* 3.3 36.9 - - + +
239I PHE* 5.8 0.2 - - + -
500I PLP 3.8 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