Contacts of the strand formed by residues 226 - 230 (chain C) in PDB entry 1C9T
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 GLY 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182C CYS* 3.3 2.9 - - - -
183C ALA 3.0 33.3 + - - -
184C GLY* 5.4 0.2 - - - -
189C ASP* 3.4 27.0 + - - -
215C TRP 4.0 2.2 - - - -
216C GLY* 4.9 2.0 - - - -
225C PRO* 1.3 75.3 - - - +
227C VAL* 1.3 60.1 + - - -
228C TYR* 3.2 12.9 - - - -
34I LYS* 4.0 11.2 - - - -
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C TYR* 3.6 37.0 - - + -
176C ILE* 3.9 11.9 - - + -
180C MET* 3.8 25.1 - - + -
181C PHE 3.6 6.7 - - - +
182C CYS* 4.1 4.0 - - - -
213C VAL* 5.4 0.3 - - - +
214C SER* 3.3 19.7 + - - -
215C TRP* 2.8 61.5 + - + +
225C PRO 3.9 0.7 - - - +
226C GLY* 1.3 72.3 - - - +
228C TYR* 1.3 70.8 + - - +
34I LYS* 5.9 0.2 + - - -
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Residues in contact with TYR 228 (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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138C ILE* 3.0 25.6 - - + +
180C MET* 3.2 6.8 - - - -
181C PHE* 2.8 62.8 + + + +
183C ALA* 3.6 26.7 + - + -
189C ASP* 3.9 7.3 + - - -
190C SER* 2.9 24.7 + - - -
199C VAL* 3.2 28.7 - - + -
212C ILE 3.4 8.5 - - - +
213C VAL* 3.4 35.7 - - + -
214C SER* 4.4 2.5 - - - +
226C GLY 3.2 25.4 - - - -
227C VAL* 1.3 79.3 - - - +
229C THR* 1.3 60.5 + - - +
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Residues in contact with THR 229 (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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101C ASN* 5.1 0.4 - - - +
102C ASP* 3.1 50.1 + - - +
103C ILE* 4.7 4.3 - - + -
179C ASN 3.5 9.6 - - - +
180C MET* 4.7 0.9 - - - +
181C PHE* 3.6 1.1 - - - -
211C GLY* 2.9 28.2 - - - -
212C ILE* 3.0 27.8 + - + +
214C SER* 4.0 3.4 - - - -
228C TYR* 1.3 71.6 - - - +
230C LYS* 1.3 63.1 + - - +
231C VAL 3.0 2.9 + - - +
234C TYR* 3.7 26.9 - - + +
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Residues in contact with LYS 230 (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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128C CYS* 4.1 13.5 - - - +
129C ALA 5.9 1.6 - - - -
178C SER* 3.3 23.8 + - - +
179C ASN 2.9 22.0 + - - +
180C MET 4.2 8.9 + - - +
181C PHE* 3.9 22.9 - - + -
210C GLN* 4.0 2.5 - - - +
228C TYR 3.6 1.6 + - - -
229C THR* 1.3 69.3 - - - +
231C VAL* 1.3 63.1 + - - +
232C CYS* 3.0 27.3 + - - -
233C ASN* 3.1 22.3 + - - +
234C TYR* 3.2 16.6 - - - -
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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