Contacts of the strand formed by residues 200 - 209 (chain C) in PDB entry 1D2H
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 LYS 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C PRO* 3.9 21.2 - - - +
189C GLY* 3.9 26.4 - - - +
196C SER* 4.9 13.3 - - - -
198C LEU* 2.8 25.0 + - + +
199C THR* 1.3 78.2 - - - +
201C ASP* 1.3 63.3 + - - +
202C ILE* 4.5 3.1 - - + -
220C TYR* 4.2 25.4 - - + -
221C THR 3.5 6.1 - - - +
222C VAL* 3.3 35.7 - - + +
223C GLN* 4.4 0.4 - - - +
235C PHE* 5.7 0.9 - - - -
238C PHE* 5.9 0.2 - - + -
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Residues in contact with ASP 201 (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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188C PRO* 5.5 0.4 - - - -
200C LYS* 1.3 72.8 - - - +
202C ILE* 1.3 91.0 + - - +
203C THR* 4.8 3.3 + - - +
220C TYR* 3.5 6.2 - - - -
221C THR* 3.0 50.8 + - + +
235C PHE* 6.0 0.9 - - + -
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Residues in contact with ILE 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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186C ALA 4.6 10.3 - - - +
188C PRO* 2.8 51.4 - - + -
200C LYS* 4.4 3.4 - - + +
201C ASP* 1.3 92.5 + - - +
203C THR* 1.3 65.6 + - - +
204C THR* 4.2 4.3 + - - +
218C LEU* 3.9 26.7 - - + -
219C ASP 3.3 8.7 - - - +
220C TYR* 3.3 41.5 - - + -
210D ASN* 4.5 5.4 + - - +
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Residues in contact with THR 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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201C ASP* 4.8 3.1 + - - +
202C ILE* 1.3 75.0 - - - +
204C THR* 1.3 60.5 + - - +
205C SER* 3.8 2.6 + - - +
217C THR 3.0 6.9 - - - +
218C LEU* 3.5 2.2 - - - -
219C ASP* 3.0 48.2 + - - +
221C THR* 4.4 6.9 + - - -
237C LYS* 5.5 2.1 - - - -
209D VAL* 4.4 11.9 - - + -
210D ASN* 2.7 35.4 - - - +
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Residues in contact with THR 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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180C ILE* 5.5 2.7 - - + -
184C GLY 4.5 2.2 - - - -
185C CYS* 3.9 15.4 - - - +
186C ALA* 3.4 31.4 + - + +
202C ILE* 4.2 4.5 + - - +
203C THR* 1.3 71.3 + - - +
205C SER* 1.3 61.5 + - - +
206C VAL* 3.9 20.0 - - + -
216C VAL* 4.0 20.2 - - + -
217C THR 3.7 2.0 - - - -
218C LEU* 4.0 11.6 - - + +
208D THR* 2.9 9.0 - - - +
210D ASN* 2.9 36.3 + - - +
211D ASN 4.5 0.2 + - - -
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Residues in contact with SER 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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203C THR* 4.5 3.5 + - - -
204C THR* 1.3 64.7 - - - +
206C VAL* 1.3 58.9 + - - +
207C LEU* 3.4 4.7 + - - +
216C VAL* 3.6 1.1 + - - -
217C THR* 3.0 48.8 + - - -
219C ASP* 4.3 9.2 + - - -
239C ARG* 4.7 6.0 + - - -
207D LEU* 3.9 16.9 - - - +
208D THR 2.4 22.0 - - - -
209D VAL* 3.6 17.6 - - - +
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Residues in contact with VAL 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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180C ILE* 5.6 3.1 - - + +
181C LEU* 5.0 15.0 - - + -
184C GLY* 4.5 18.6 - - - +
204C THR* 3.9 21.8 - - + -
205C SER* 1.3 69.6 - - - +
207C LEU* 1.3 66.1 + - - +
208C THR* 4.2 7.8 + - - +
213C ALA* 5.2 4.7 - - + -
215C MET 3.6 14.4 - - - +
216C VAL* 3.9 14.6 - - + +
206D VAL* 3.7 4.2 - - - +
208D THR* 2.9 50.3 + - + -
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Residues in contact with LEU 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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205C SER 3.4 4.8 + - - +
206C VAL* 1.3 75.9 - - - +
208C THR* 1.3 75.8 + - - +
209C VAL* 4.1 7.2 - - + -
213C ALA* 3.7 3.1 - - - -
214C HIS* 3.0 35.4 + - + -
215C MET* 3.0 53.2 + - + +
217C THR* 5.9 0.2 - - - +
205D SER* 3.8 25.1 - - - +
206D VAL 3.7 11.9 - - - +
207D LEU* 4.4 14.4 - - + -
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Residues in contact with THR 208 (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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206C VAL* 4.2 8.7 + - - +
207C LEU* 1.3 78.1 + - - +
209C VAL* 1.3 61.7 + - - +
211C ASN* 3.6 37.2 - - - +
212C LYS 3.8 6.3 - - - +
213C ALA* 4.3 5.5 - - - +
184D GLY* 5.2 6.5 - - - +
204D THR 3.6 2.6 - - - +
205D SER* 3.3 4.5 - - - -
206D VAL* 2.9 48.0 + - + +
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Residues in contact with VAL 209 (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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207C LEU* 4.1 9.2 - - + -
208C THR* 1.3 71.0 - - - +
210C ASN* 1.3 77.0 + - + +
211C ASN 3.2 0.2 - - - -
212C LYS* 3.0 34.5 + - + +
214C HIS* 3.7 40.1 - - + +
203D THR* 4.0 22.9 - - + -
204D THR 3.9 2.5 - - - -
205D SER* 3.5 19.3 - - - +
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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