Contacts of the strand formed by residues 205 - 209 (chain D) in PDB entry 1UMD
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 LEU 205 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LYS 3.6 1.2 - - - -
204D ASP* 1.3 84.0 - - + +
206D THR* 1.3 92.0 + - - +
207D LEU* 4.1 11.7 - - + -
224D LEU* 4.1 15.3 - - + -
229D VAL* 5.0 2.2 - - + -
230D SER 3.4 2.4 + - - +
231D ALA* 3.3 7.2 - - - -
232D GLU* 2.6 35.5 + - - +
254D THR* 3.7 6.7 - - - +
256D ARG* 3.4 20.4 - - + +
257D VAL* 3.9 6.5 - - - -
258D VAL* 3.9 10.8 - - + +
318D ALA* 3.6 38.4 - - + +
321D ALA* 5.0 1.8 - - + -
322D LEU* 4.4 13.5 - - + -
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Residues in contact with THR 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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205D LEU* 1.3 93.4 - - - +
207D LEU* 1.3 63.1 + - - +
208D ILE* 3.8 24.0 - - + -
232D GLU* 3.5 5.8 - - - +
234D LEU* 5.1 5.6 - - + -
250D SER* 2.8 39.6 + - - +
251D VAL* 4.4 6.3 - - + -
254D THR* 2.7 22.9 + - - +
256D ARG 2.8 10.7 + - - -
257D VAL* 3.3 8.1 - - + -
258D VAL 3.0 16.6 + - - +
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Residues in contact with LEU 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D LEU* 4.1 13.9 - - + -
206D THR* 1.3 74.6 - - - +
208D ILE* 1.3 63.1 + - - +
209D CYS* 3.8 3.6 + - - -
217D VAL* 3.9 36.6 - - + +
220D ALA* 5.0 4.0 - - + -
221D ALA* 4.2 7.2 - - + +
224D LEU* 4.7 4.3 - - + -
231D ALA* 3.8 28.3 - - + -
232D GLU 2.7 13.3 + - - +
233D VAL* 3.6 9.4 - - + -
234D LEU 3.0 26.7 + - - +
258D VAL* 3.4 31.2 - - + +
260D VAL* 5.0 3.1 - - + -
314D ILE* 4.6 12.8 - - + -
318D ALA* 5.2 2.7 - - + -
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Residues in contact with ILE 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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206D THR* 3.8 13.2 - - + -
207D LEU* 1.3 70.0 - - - +
209D CYS* 1.3 65.8 + - - +
210D TYR* 6.1 0.2 - - + -
234D LEU* 3.8 9.2 - - + -
236D LEU* 3.8 33.7 - - + -
247D VAL* 3.7 31.9 - - + -
251D VAL* 4.5 3.1 - - + -
257D VAL* 3.5 26.0 - - + -
258D VAL 3.0 6.5 + - - +
259D LEU* 3.3 23.9 - - + +
260D VAL* 2.8 28.2 + - - +
270D VAL* 5.5 3.9 - - + +
273D VAL* 4.2 3.4 - - + -
277D ILE* 3.7 11.2 - - + -
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Residues in contact with CYS 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 LEU 3.9 1.3 - - - -
208D ILE* 1.3 80.3 - - - +
210D TYR* 1.3 69.9 + - - +
213D VAL* 4.0 2.0 - - + -
214D MET* 3.2 37.2 - - - -
217D VAL* 3.7 35.2 - - + -
233D VAL* 3.8 8.1 - - - -
234D LEU 3.1 13.9 + - - +
235D ASP* 3.4 0.7 - - - -
236D LEU* 2.9 28.1 + - - +
260D VAL* 3.6 15.7 - - + +
270D VAL* 6.1 0.4 - - - -
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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