Contacts of the strand formed by residues 257 - 264 (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 VAL 257 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LEU* 3.9 0.4 - - - -
206D THR* 3.3 14.6 - - + +
208D ILE* 3.5 35.0 - - + -
251D VAL* 4.0 20.0 - - + -
256D ARG* 1.3 77.9 - - - +
258D VAL* 1.3 71.2 + - - +
259D LEU* 3.7 10.8 - - + -
277D ILE* 4.2 15.3 - - + -
285D LEU* 4.5 5.4 - - + -
287D ALA 5.4 0.2 + - - -
288D PRO 3.9 5.2 + - - +
289D PRO* 3.6 25.1 - - + +
290D ILE* 3.1 22.3 + - - +
321D ALA* 4.9 1.9 - - - +
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D LEU* 4.2 9.4 - - + -
206D THR 3.0 4.9 + - - -
207D LEU* 3.4 20.1 - - + +
208D ILE 3.0 23.4 + - - +
257D VAL* 1.3 78.9 - - - +
259D LEU* 1.3 63.2 + - - +
260D VAL* 4.0 13.5 + - + +
290D ILE* 3.2 15.0 - - + +
292D VAL* 3.9 25.4 - - + -
314D ILE* 4.8 4.0 - - + +
317D ALA* 3.9 26.9 - - + +
318D ALA* 4.0 13.5 - - - -
321D ALA* 4.2 7.9 - - + -
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Residues in contact with LEU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 3.3 25.4 - - + +
257D VAL* 3.7 24.5 - - + +
258D VAL* 1.3 72.2 - - - +
260D VAL* 1.3 60.3 + - - +
270D VAL* 3.5 38.8 - - + +
273D VAL* 3.7 29.8 - - + -
274D ALA* 3.8 18.8 - - + +
277D ILE* 4.4 1.8 - - + -
289D PRO* 4.4 4.9 - - + -
290D ILE 2.8 21.4 + - - +
291D ARG* 3.4 5.6 - - + +
292D VAL 2.7 32.7 + - - +
293D THR* 5.0 0.7 - - - +
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Residues in contact with VAL 260 (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* 5.0 4.7 - - + -
208D ILE 2.8 13.4 + - - +
209D CYS* 3.6 18.9 - - + -
210D TYR* 4.2 2.8 + - - -
213D VAL* 3.6 26.5 - - + +
217D VAL* 3.8 24.7 - - + -
258D VAL* 4.0 19.7 - - + +
259D LEU* 1.3 79.3 - - - +
261D SER* 1.3 67.5 + - - +
270D VAL* 4.1 4.6 - - - +
292D VAL* 3.2 18.4 - - + +
309D PRO* 4.2 3.6 - - + -
314D ILE* 4.0 26.5 - - + -
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Residues in contact with SER 261 (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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134D GLU* 3.9 1.4 + - - -
210D TYR* 3.1 26.9 + - - -
213D VAL* 3.6 14.1 - - - -
260D VAL* 1.3 78.5 - - - +
262D ASP* 1.3 62.3 + - - +
263D ALA* 3.1 18.8 + - - +
270D VAL* 3.7 27.3 - - - +
292D VAL 3.1 5.3 + - - +
293D THR* 3.0 26.3 - - - +
294D GLY 3.4 0.2 + - - -
309D PRO* 3.6 4.0 - - - +
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Residues in contact with ASP 262 (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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120D GLY* 3.5 0.2 - - - -
121D GLY* 3.1 29.1 + - - -
130D SER 4.2 2.1 - - - +
132D SER* 2.7 26.1 + - - -
134D GLU* 4.8 1.4 - - - +
210D TYR* 6.1 0.5 - - - -
212D THR* 3.7 19.1 + - - +
213D VAL* 3.5 7.5 - - + +
261D SER* 1.3 73.9 + - - +
263D ALA* 1.3 65.8 + - - +
264D PRO* 4.3 0.5 - - - +
294D GLY 3.8 2.5 - - - +
299D TYR* 4.3 5.4 - - + -
307D TYR* 3.4 24.3 + - + -
308D LEU* 3.8 25.6 - - + +
309D PRO* 4.0 10.1 - - + -
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Residues in contact with ALA 263 (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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139B HIS* 4.7 5.6 - - + +
132D SER* 3.6 22.2 - - - +
134D GLU* 3.6 15.5 - - + +
135D ALA* 6.0 1.1 - - + +
210D TYR* 4.6 1.1 - - - +
261D SER* 3.1 14.6 + - - +
262D ASP* 1.3 80.8 + - - +
264D PRO* 1.3 79.6 - - + +
268D SER* 4.8 7.3 - - - -
269D PHE 5.9 1.1 - - - +
270D VAL* 5.9 0.2 - - - +
293D THR* 3.5 7.1 - - - +
294D GLY 2.9 16.0 + - - -
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Residues in contact with PRO 264 (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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139B HIS* 3.4 39.6 - - + +
141B ALA* 6.0 2.5 - - + +
132D SER* 4.2 8.7 - - - +
262D ASP 3.8 0.9 - - - +
263D ALA* 1.3 87.1 - - + +
265D ARG* 1.3 65.6 + - - +
266D HIS 3.7 0.4 - - - +
268D SER* 3.0 20.8 - - - -
294D GLY 3.7 7.0 - - - +
295D PHE 3.8 9.0 - - - +
296D ASP* 4.1 9.4 - - - +
297D THR 4.8 6.5 - - - +
307D TYR* 3.7 15.7 - - - +
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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