Contacts of the strand formed by residues 200 - 209 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A PRO* 4.5 15.0 - - + +
189A GLY* 3.7 40.3 + - - +
196A SER* 5.4 4.8 + - - -
198A LEU* 2.6 32.9 + - + +
199A THR* 1.3 82.2 - - - +
201A ASP* 1.3 65.5 + - - +
202A ILE* 4.2 9.6 + - + -
220A TYR* 4.6 16.4 - - + -
221A THR 3.5 8.5 - - - +
222A VAL* 3.6 24.9 - - + -
238A PHE* 6.0 0.7 - - + -
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Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PRO* 5.6 0.2 - - - -
200A LYS* 1.3 73.3 - - - +
202A ILE* 1.3 70.2 + - - +
203A THR* 6.1 0.2 - - - -
219A ASP 3.4 1.2 - - - +
220A TYR* 3.4 5.0 - - - -
221A THR* 3.0 48.6 + - + +
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Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A CYS* 5.9 1.6 - - - -
186A ALA* 4.3 10.1 - - + +
188A PRO* 2.8 47.2 - - + +
200A LYS* 4.4 3.3 + - + -
201A ASP* 1.3 90.9 + - - +
203A THR* 1.3 76.7 + - - +
204A THR* 4.0 8.8 + - - +
218A LEU* 4.0 23.8 - - + -
219A ASP 3.1 9.2 - - - +
220A TYR* 3.6 34.5 - - + -
210B ASN* 5.2 3.6 + - - +
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Residues in contact with THR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 6.1 0.3 - - - -
202A ILE* 1.3 81.2 + - - +
204A THR* 1.3 62.2 + - - +
205A SER* 3.4 15.4 + - - +
217A THR 3.4 2.8 - - - +
219A ASP* 3.0 40.4 + - - +
209B VAL* 5.8 5.2 - - + -
210B ASN* 3.8 23.0 + - - +
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ILE* 5.4 2.9 - - + -
184A GLY 3.9 7.5 - - - +
185A CYS* 3.4 21.9 - - - +
186A ALA* 2.7 38.4 + - + +
202A ILE* 4.0 6.3 + - - +
203A THR* 1.3 71.0 - - - +
205A SER* 1.3 59.5 + - - +
206A VAL* 3.9 9.0 + - + +
216A VAL* 4.0 12.8 - - + -
218A LEU* 3.1 27.1 - - + +
210B ASN* 3.0 31.0 + - - -
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A THR* 3.5 12.0 + - - +
204A THR* 1.3 70.9 - - - +
206A VAL* 1.3 65.1 + - - +
207A LEU* 5.4 0.3 - - - +
215A MET 5.0 0.2 - - - -
216A VAL* 4.6 0.2 - - - -
217A THR* 2.9 49.5 + - - -
219A ASP* 3.9 10.0 + - - -
239A ARG* 5.6 0.2 + - - -
207B LEU* 5.3 8.6 - - - +
208B THR 3.5 11.2 - - - -
209B VAL* 4.1 17.7 - - - +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ILE* 5.8 1.6 - - + +
181A LEU* 4.3 20.4 - - + -
184A GLY* 4.4 18.8 - - - +
204A THR* 3.9 18.5 + - + -
205A SER* 1.3 73.7 - - - +
207A LEU* 1.3 80.5 + - - +
208A THR* 4.7 5.4 - - - +
213A ALA* 4.9 5.2 - - + -
215A MET 3.6 13.5 - - - +
216A VAL* 3.9 17.9 - - + +
207B LEU* 3.6 6.7 - - - +
208B THR* 2.9 45.3 + - + +
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A SER 5.4 0.4 - - - +
206A VAL* 1.3 80.6 - - - +
208A THR* 1.3 71.9 + - - +
209A VAL* 5.0 1.8 - - + +
213A ALA* 3.4 5.5 - - - -
214A HIS* 3.0 29.6 + - + -
215A MET* 3.1 50.7 + - + +
217A THR* 6.0 0.9 - - - +
205B SER* 4.6 10.5 - - - +
206B VAL 2.7 36.3 - - - +
207B LEU* 4.1 17.0 - - + -
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL* 4.7 5.7 - - - +
207A LEU* 1.3 80.2 + - - +
209A VAL* 1.3 59.8 + - - +
210A ASN 3.6 1.4 + - - -
211A ASN* 3.2 43.0 + - - +
212A LYS 3.6 5.8 - - - +
213A ALA* 4.1 3.8 - - + +
184B GLY* 5.1 2.5 - - - +
204B THR 4.0 0.2 - - - +
205B SER* 3.5 1.6 - - - -
206B VAL* 2.9 49.9 + - + +
208B THR* 5.0 7.4 + - - -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LEU* 4.2 2.8 - - + -
208A THR* 1.3 69.6 - - - +
210A ASN* 1.3 73.9 + - + +
211A ASN 3.1 0.9 - - - -
212A LYS* 2.9 53.2 + - - +
214A HIS* 3.3 32.1 - - + +
203B THR* 5.0 12.3 - - + -
204B THR 3.9 7.0 - - - +
205B SER* 4.5 14.1 - - - +
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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