Contacts of the strand formed by residues 205 - 209 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B LYS 3.6 1.0 - - - -
204B ASP* 1.3 81.5 - - + +
206B THR* 1.3 66.8 + - - +
207B LEU* 4.3 14.8 - - + -
224B LEU* 4.2 15.3 - - + -
229B VAL* 5.1 1.1 - - + -
230B SER 3.4 2.0 + - - -
231B ALA* 3.3 7.2 - - + -
232B GLU* 2.7 35.7 + - - +
254B THR* 3.8 4.5 - - - +
256B ARG* 3.5 37.0 - - + +
257B VAL 4.0 2.0 - - - +
258B VAL* 4.2 5.6 - - + -
318B ALA* 3.6 34.5 - - + +
321B ALA* 4.0 16.4 - - + -
322B LEU* 4.3 12.3 - - + -
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 1.3 76.2 - - - +
207B LEU* 1.3 64.4 - - - +
208B ILE* 3.8 23.8 - - + -
232B GLU 3.5 6.1 - - - +
234B LEU* 5.2 4.9 - - + -
247B VAL 5.4 0.2 - - - +
250B SER* 2.8 38.4 + - - +
251B VAL* 4.4 6.1 - - + -
254B THR* 2.6 24.5 + - - +
256B ARG 2.9 15.1 + - - -
257B VAL* 3.2 9.9 - - + +
258B VAL 2.9 27.0 + - - +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.3 11.7 - - + -
206B THR* 1.3 74.1 - - - +
208B ILE* 1.3 63.1 + - - +
209B CYS* 3.9 2.8 + - - -
217B VAL* 4.0 32.8 - - + +
220B ALA* 5.1 3.8 - - + -
221B ALA* 4.3 8.3 - - + +
224B LEU* 4.6 5.8 - - + -
231B ALA* 4.1 20.2 - - + -
232B GLU 2.8 13.0 + - - +
233B VAL* 3.6 16.8 - - + -
234B LEU* 2.9 26.7 + - - +
258B VAL* 3.4 32.8 - - + +
260B VAL* 4.9 3.8 - - + -
314B ILE* 4.5 13.5 - - + -
318B ALA* 5.3 2.2 - - + -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 3.8 19.3 - - + -
207B LEU* 1.3 69.5 - - - +
209B CYS* 1.3 67.3 + - - +
234B LEU* 3.8 9.9 - - + +
236B LEU* 3.7 35.4 - - + -
247B VAL* 3.7 32.3 - - + -
251B VAL* 4.4 0.9 - - + -
257B VAL* 3.5 22.2 - - + -
258B VAL 3.0 6.7 + - - +
259B LEU* 3.3 23.2 - - + +
260B VAL* 2.8 28.8 + - - +
270B VAL* 5.5 2.8 - - + +
273B VAL* 4.3 3.6 - - + -
277B ILE* 3.8 9.9 - - + -
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Residues in contact with CYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU 4.1 1.6 - - - -
208B ILE* 1.3 79.0 - - - +
210B TYR* 1.3 68.8 + - - +
213B VAL* 4.0 2.7 - - + -
214B MET* 3.2 34.1 - - - -
217B VAL* 3.6 37.9 - - + -
233B VAL* 4.0 6.5 - - - -
234B LEU 3.1 13.9 + - - +
235B ASP* 3.4 0.5 - - - -
236B LEU* 3.0 27.8 + - - +
260B VAL* 3.5 17.0 - - + +
270B 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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