Contacts of the strand formed by residues 201 - 207 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C HIS* 4.1 12.8 - - + +
157C VAL* 3.5 38.6 - - + +
195C ALA 3.7 22.2 - - - +
196C LEU* 3.8 29.9 + - + +
199C LYS 3.3 1.6 + - - +
200C LYS* 1.3 75.7 - - - +
202C ASN* 1.3 62.7 + - - +
203C LEU 3.7 20.6 - - - +
204C PHE* 4.5 2.0 - - + +
229C LYS 4.9 3.3 - - - +
230C GLY 4.5 2.6 - - - +
231C ALA* 3.5 25.8 + - + +
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Residues in contact with ASN 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU 5.4 0.9 + - - +
150C VAL* 4.6 8.1 - - + -
151C PRO* 3.7 31.3 - - + +
154C GLY* 3.2 13.2 - - - -
155C HIS 2.9 36.7 + - - +
200C LYS* 3.5 16.0 + - - +
201C VAL* 1.3 74.1 - - - +
203C LEU* 1.3 66.0 + - + +
230C GLY 4.4 2.5 - - - +
231C ALA* 3.7 2.4 - - - -
232C LEU* 3.0 23.4 + - - +
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Residues in contact with LEU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C MET* 4.0 17.5 - - + -
146C LEU* 4.0 13.0 - - + -
149C LEU* 4.5 18.6 - - + -
150C VAL* 4.0 8.5 - - + -
155C HIS 3.9 1.2 + - - -
156C ILE* 3.3 31.2 - - + +
157C VAL 3.2 21.5 + - - -
201C VAL* 3.6 6.6 - - - +
202C ASN* 1.3 86.5 - - + +
204C PHE* 1.3 63.8 + - - +
205C PHE* 4.1 10.1 - - + -
232C LEU* 3.1 29.2 - - + +
234C CYS* 4.1 16.8 - - + -
254C LEU* 4.9 1.3 - - + -
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Residues in contact with PHE 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C VAL* 3.3 38.1 - - + -
158C THR* 4.3 8.1 - - - -
159C THR* 4.5 6.5 - - + -
184C ILE* 4.6 8.3 - - + -
192C LEU* 3.7 18.8 - - + -
201C VAL* 4.5 2.8 - - + +
203C LEU* 1.3 72.9 - - - +
205C PHE* 1.3 64.7 + - - +
206C THR* 3.5 30.5 - - + -
217C VAL* 4.6 4.7 - - + -
222C VAL* 3.3 44.2 - - + -
226C CYS* 3.7 17.5 - - - -
231C ALA* 4.9 0.4 - - + +
232C LEU 2.5 13.7 + - - +
233C VAL* 3.4 9.2 - - + -
234C CYS 2.9 25.6 + - - +
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Residues in contact with PHE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C SER* 4.7 8.7 - - - -
145C MET* 4.5 10.3 - - + -
146C LEU* 5.1 5.4 - - + -
156C ILE* 4.8 2.7 - - + -
157C VAL 2.9 7.1 + - - -
158C THR* 3.0 44.1 - - + +
162C CYS* 4.2 12.1 - - - -
166C THR* 3.9 28.9 - - + -
170C ILE* 5.0 3.8 - - + -
203C LEU* 3.8 16.9 + - + -
204C PHE* 1.3 75.0 - - - +
206C THR* 1.3 69.8 + - - +
207C GLU* 4.4 9.0 - - - -
234C CYS* 3.5 27.4 - - + -
236C ASP* 4.4 20.6 - - + -
256C LEU* 3.5 31.0 - - + -
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Residues in contact with THR 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C THR* 3.2 31.6 + - - +
162C CYS* 6.0 2.2 - - - -
204C PHE* 3.5 30.5 - - + -
205C PHE* 1.3 85.0 - - - +
207C GLU* 1.3 77.1 + - - +
210C THR* 5.2 0.3 + - - -
217C VAL* 4.1 13.8 - - + +
234C CYS 3.0 4.5 + - - +
235C ILE* 3.0 30.0 - - + -
236C ASP* 2.8 22.2 + - - -
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Residues in contact with GLU 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C THR* 5.7 0.4 - - - +
161C ASP 3.7 7.1 - - - +
162C CYS* 4.3 8.0 - - - -
163C TYR* 3.3 32.7 + - - +
205C PHE* 4.4 12.6 - - - -
206C THR* 1.3 86.6 + - - +
208C SER* 1.3 65.8 + - - +
209C PRO 3.4 10.5 - - - +
210C THR* 3.6 22.3 + - - +
211C ASN* 4.0 8.9 + - - +
215C ARG 4.4 2.3 - - - +
217C VAL* 4.6 3.5 - - - +
236C ASP* 3.2 35.9 - - + +
500C PLP 3.7 22.6 - - + +
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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