Contacts of the strand formed by residues 200 - 214 (chain D) in PDB entry 1DVM
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 PRO 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D THR* 4.7 8.3 - - + -
185D HIS 3.8 5.6 - - - +
186D ARG* 3.7 31.9 - - - +
199D VAL* 1.4 88.0 - - + +
201D MET* 1.3 59.8 + - - +
276D PRO* 3.6 3.3 - - - +
277D LYS* 3.3 47.1 + - + +
379D PRO* 6.0 1.8 - - + -
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Residues in contact with MET 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D THR* 4.3 2.4 - - - +
185D HIS* 2.6 50.2 + - + +
187D ARG* 3.3 39.9 - - + +
188D LEU 3.9 3.8 - - - +
189D PHE* 4.1 13.2 - - + -
199D VAL* 3.5 4.7 + - + +
200D PRO* 1.3 72.8 - - - +
202D MET* 1.3 59.1 + - - +
274D VAL* 3.7 14.6 - - + -
275D LEU 3.5 2.9 - - - +
276D PRO* 3.4 22.0 - - + -
353D ILE* 3.4 25.6 - - - -
354D ILE 4.0 8.1 - - - +
355D ASP* 3.8 28.3 - - + -
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Residues in contact with MET 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D TRP* 4.1 1.8 - - - +
179D PHE* 3.7 37.0 - - + -
184D THR* 3.3 25.7 - - + +
200D PRO 4.2 1.4 + - - -
201D MET* 1.3 74.0 - - - +
203D ALA* 1.3 59.4 + - - +
274D VAL* 3.6 1.1 - - - -
275D LEU* 2.8 53.9 + - + +
276D PRO 4.5 0.9 - - - +
277D LYS* 3.8 13.4 - - + +
328D VAL* 3.6 25.6 - - + -
329D ASN* 3.3 40.6 - - - +
330D GLU* 3.4 11.9 - - - +
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Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D PHE* 3.4 7.3 - - - +
180D PRO* 3.4 17.7 + - - +
183D SER* 3.8 32.0 + - - +
184D THR 4.7 0.2 - - - +
185D HIS* 4.3 8.3 - - + -
201D MET 3.9 0.8 + - - -
202D MET* 1.3 74.7 - - - +
204D GLN* 1.3 65.3 + - - +
272D LEU* 4.2 8.7 - - + -
273D LEU 3.3 14.4 - - - +
274D VAL* 4.0 15.0 - - + -
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Residues in contact with GLN 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D THR* 3.2 43.4 + - + +
178D PRO 4.3 1.6 - - - +
179D PHE* 3.4 31.6 - - + -
180D PRO* 3.8 20.6 - - + -
183D SER* 5.8 0.2 - - - -
203D ALA* 1.3 80.5 - - - +
205D THR* 1.3 69.0 + - - +
206D ASN* 3.3 23.8 + - - +
208D PHE* 3.1 22.8 - - - -
226D LEU* 5.7 0.2 - - - +
272D LEU* 4.3 1.2 - - - +
273D LEU 3.0 25.1 + - - +
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Residues in contact with THR 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLU* 5.8 2.5 - - - +
204D GLN* 1.3 78.3 - - - +
206D ASN* 1.3 70.1 + - - +
271D ARG 3.2 12.8 - - - -
272D LEU* 3.2 36.8 - - + -
345D ALA* 4.8 13.1 - - + +
346D ARG* 2.7 38.9 + - - +
347D MET* 5.7 0.2 - - - -
348D ALA* 4.3 7.3 - - + +
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Residues in contact with ASN 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D THR* 4.4 12.9 + - - +
204D GLN* 3.3 19.8 + - - +
205D THR* 1.3 74.9 + - - +
207D LYS* 1.3 72.8 + - - +
208D PHE* 2.8 47.0 + - - -
270D PRO* 3.3 3.6 - - - +
271D ARG 3.0 31.5 + - - +
348D ALA* 5.5 0.6 - - - +
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Residues in contact with LYS 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 6.0 4.5 - - - +
206D ASN* 1.3 85.8 + - - +
208D PHE* 1.3 63.9 + - - +
209D ASN 4.0 1.4 + - - -
268D ARG* 3.9 42.5 + - + +
269D LEU 3.9 2.7 - - - -
270D PRO* 4.3 22.9 - - + +
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Residues in contact with PHE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D GLN* 3.1 37.5 - - - -
206D ASN* 2.8 30.3 + - - -
207D LYS* 1.3 73.0 - - - +
209D ASN* 1.3 61.5 + - - +
210D TYR* 3.3 4.2 + - - +
224D LEU* 3.9 21.3 - - + -
225D GLU 4.7 11.0 - - - +
226D LEU* 4.6 8.1 - - + -
268D ARG* 3.9 1.8 - - - -
269D LEU* 2.8 36.8 + - - +
271D ARG* 3.1 41.1 - - + -
273D LEU* 3.5 37.9 - - + -
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Residues in contact with ASN 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LYS 4.0 2.8 + - - -
208D PHE* 1.3 69.3 - - - +
210D TYR* 1.3 59.3 + - - +
224D LEU* 3.6 4.7 - - - +
225D GLU* 3.0 63.1 + - + +
263D LYS* 5.0 1.6 + - - +
266D MET* 3.2 36.2 - - - +
267D THR* 3.5 7.6 + - - -
268D ARG* 3.3 35.8 + - + +
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Residues in contact with TYR 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D PHE 3.9 3.6 - - - +
209D ASN* 1.3 75.4 - - - +
211D THR* 1.3 60.3 + - - +
212D GLU* 3.6 33.4 - - + +
222D ASP* 2.8 43.7 + - + -
223D ILE 3.3 20.2 - - - -
224D LEU* 3.8 18.8 - - + -
265D ASN 4.0 0.9 - - - +
266D MET* 3.5 3.7 - - - -
267D THR* 2.6 41.9 + - - +
269D LEU* 3.9 23.5 - - + +
271D ARG* 5.9 2.0 - - + -
352D ILE* 4.2 17.3 - - + -
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Residues in contact with THR 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D TYR* 1.3 84.9 - - - +
212D GLU* 1.3 66.9 + - - +
213D PHE* 5.2 0.4 - - + -
223D ILE* 3.0 47.8 + - + +
262D TRP* 4.0 15.7 - - + +
265D ASN* 3.3 35.6 + - - +
266D MET* 3.8 17.7 - - + -
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Residues in contact with GLU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ARG* 3.5 36.6 + - - -
210D TYR* 3.6 24.2 + - + +
211D THR* 1.3 80.0 + - - +
213D PHE* 1.3 67.0 + - - +
214D THR* 4.2 8.4 + - - +
220D TYR* 4.0 25.1 - - + +
221D TYR 3.4 13.7 - - - +
222D ASP* 4.7 2.9 - - - +
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Residues in contact with PHE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C LEU* 4.2 10.1 - - + -
211D THR* 3.7 2.0 + - + +
212D GLU* 1.3 75.1 - - - +
214D THR* 1.3 81.2 + - - +
215D THR* 3.4 31.6 - - + -
216D PRO* 5.0 0.7 - - + -
219D HIS 3.2 1.7 - - - +
220D TYR* 3.1 2.3 - - - -
221D TYR* 2.6 53.6 + + + -
223D ILE* 3.4 23.1 - - + -
250D LEU* 3.6 19.7 - - + -
253D ILE* 4.0 7.6 - - + -
258D LEU* 3.7 26.2 - - + -
261D HIS* 4.1 18.2 - + - -
262D TRP* 3.5 22.0 - + + +
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Residues in contact with THR 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ARG* 5.4 2.7 - - + -
152C LEU* 5.7 0.5 - - - +
212D GLU* 4.6 10.8 - - - +
213D PHE* 1.3 94.7 - - - +
215D THR* 1.3 70.5 + - - +
216D PRO* 4.2 1.4 - - - +
218D GLY* 4.4 3.6 - - - -
219D HIS 3.1 5.6 - - - -
220D TYR* 3.2 40.8 - - + -
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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