Contacts of the helix formed by residues 253 - 268 (chain B) in PDB entry 3UMO
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 GLY 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ASN* 6.1 0.9 - - - -
105B ARG* 4.6 2.4 - - - +
251B THR 3.3 0.8 + - - -
252B VAL* 1.3 79.8 - - - +
254B ALA* 1.3 63.3 + - - +
255B GLY 3.3 1.8 - - - -
256B ASP* 3.7 10.7 + - - -
257B SER* 2.9 30.4 + - - -
286B ALA* 4.1 3.1 - - - -
292B THR 5.1 0.2 - - - -
294B LEU* 3.8 19.7 - - - +
313B ATP 3.8 9.6 + - - -
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR* 3.1 17.5 + - - +
252B VAL 3.3 1.4 + - - -
253B GLY* 1.3 78.1 - - - +
255B GLY* 1.3 64.3 + - - +
257B SER 3.4 0.5 + - - -
258B MET* 3.0 21.3 + - - +
283B GLY* 3.4 24.3 - - - +
286B ALA* 3.8 3.8 - - + +
287B THR* 4.1 4.9 - - + -
313B ATP 3.3 41.8 + - + +
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 4.7 1.8 - - - -
185B LYS* 4.0 6.0 - - - -
254B ALA* 1.3 77.7 - - - +
256B ASP* 1.3 58.7 + - - +
258B MET* 3.3 3.3 + - - +
259B VAL* 3.0 33.9 + - - +
311B MG 4.5 0.2 - - - -
313B ATP 3.1 48.1 + - - -
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Residues in contact with ASP 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLY 4.8 0.2 - - - -
40B GLY* 3.7 24.0 - - - +
43B ASN* 3.3 40.9 + - + +
44B VAL* 3.9 16.2 - - + +
47B ALA* 4.0 5.7 - - - +
137B SER* 4.0 7.1 + - - -
166B ASP* 4.4 5.7 - - - +
253B GLY* 3.7 12.2 + - - +
254B ALA 3.4 0.2 - - - -
255B GLY* 1.3 73.1 - - - +
257B SER* 1.3 60.6 + - - +
259B VAL* 3.3 2.3 + - - +
260B GLY* 2.9 26.5 + - - -
294B LEU* 4.8 3.4 - - + -
313B ATP 4.5 6.3 + - - -
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Residues in contact with SER 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 3.8 12.8 - - - +
51B LEU* 4.7 0.2 - - - +
253B GLY 2.9 23.0 + - - -
254B ALA 3.7 3.1 - - - -
256B ASP* 1.3 78.1 - - - +
258B MET* 1.3 62.4 + - - +
260B GLY* 3.4 0.5 + - - -
261B ALA* 3.0 23.4 + - - +
282B ALA* 3.5 27.6 - - - +
286B ALA* 3.5 3.8 - - - +
294B LEU* 3.6 8.7 - - - +
295B CYS* 3.3 30.0 + - - -
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Residues in contact with MET 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LYS* 3.6 24.0 - - + -
222B VAL* 4.7 0.7 - - - -
224B SER* 3.8 14.8 - - - -
230B ALA* 3.9 10.3 - - + -
254B ALA 3.0 17.6 + - - +
255B GLY 3.3 4.2 + - - +
257B SER* 1.3 75.9 - - - +
259B VAL* 1.3 57.7 + - - +
261B ALA* 3.3 2.4 + - - +
262B MET* 2.9 48.7 + - + +
276B VAL 4.8 1.1 - - - +
279B GLY* 3.4 46.2 - - - +
280B VAL* 3.4 17.5 - - + +
283B GLY* 4.0 3.5 - - - +
313B ATP 3.1 27.6 - - - +
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Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.8 12.6 - - + -
135B VAL* 3.8 29.2 - - + -
164B ILE* 4.5 10.5 - - + -
166B ASP* 3.4 27.4 - - + +
183B LEU* 5.6 0.8 - - + +
185B LYS* 3.6 27.4 - - + -
255B GLY 3.0 20.2 + - - +
256B ASP 3.8 4.0 - - - +
257B SER 3.3 0.2 - - - -
258B MET* 1.3 77.3 - - - +
260B GLY* 1.3 54.3 + - - +
262B MET* 3.3 7.4 + - + +
263B THR* 2.7 42.5 + - - +
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Residues in contact with GLY 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.8 14.8 - - - +
47B ALA* 4.6 3.1 - - - -
48B ILE* 3.5 32.9 - - - +
51B LEU* 4.6 3.1 - - - -
256B ASP 2.9 14.6 + - - -
257B SER 3.8 1.1 - - - -
258B MET 3.3 0.2 - - - -
259B VAL* 1.3 76.6 - - - +
261B ALA* 1.3 61.4 + - - +
263B THR* 3.4 1.4 + - - -
264B LEU* 3.1 20.1 + - - +
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.8 13.0 - - + +
257B SER 3.0 7.0 + - - +
258B MET 3.5 4.5 - - - +
260B GLY* 1.3 76.4 - - - +
262B MET* 1.3 63.0 + - - +
264B LEU* 3.3 3.4 + - - +
265B LYS* 3.1 17.2 + - - +
278B PHE* 3.4 39.9 - - + +
279B GLY* 4.0 0.7 - - - -
282B ALA* 3.4 31.9 - - + -
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Residues in contact with MET 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LEU* 4.0 18.4 - - + -
185B LYS* 4.0 18.8 - - + -
222B VAL* 3.8 44.6 - - + -
258B MET* 2.9 38.6 + - + +
259B VAL* 4.0 7.0 - - + +
261B ALA* 1.3 76.6 - - - +
263B THR* 1.3 52.1 + - - +
265B LYS* 3.1 3.2 + - - +
266B LEU* 2.8 35.7 + - - +
275B MET* 3.4 41.9 - - + +
276B VAL* 4.4 4.5 - - - -
279B GLY* 3.6 9.0 - - - -
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Residues in contact with THR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.7 27.6 - - + -
48B ILE* 4.2 4.5 - - + -
133B ILE* 4.0 7.9 - - + +
135B VAL* 3.4 33.5 - - + +
164B ILE* 3.5 22.8 - - + +
183B LEU* 5.4 0.2 - - - +
259B VAL* 2.7 28.0 + - - +
260B GLY* 3.5 7.2 - - - -
262B MET* 1.3 76.9 - - - +
264B LEU* 1.3 57.3 + - - +
266B LEU* 3.2 3.4 + - - +
267B ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.1 18.2 - - + +
4B ILE* 3.8 20.6 - - + -
48B ILE* 3.9 26.0 - - + +
51B LEU* 3.8 37.7 - - + +
53B GLY* 4.2 14.1 - - - +
54B SER 5.0 0.4 - - - +
260B GLY 3.1 18.1 + - - +
261B ALA 3.3 7.4 + - - +
263B THR* 1.3 75.8 - - - +
265B LYS* 1.3 61.6 + - - +
267B ALA* 3.2 6.3 + - - +
268B GLU* 3.1 36.1 + - - +
278B PHE* 4.6 8.7 - - + -
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Residues in contact with LYS 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ALA 3.1 7.3 + - - +
262B MET 3.6 6.3 - - - +
264B LEU* 1.3 72.8 - - - +
266B LEU* 1.3 65.5 + - - +
268B GLU* 3.1 27.9 + - - +
270B ALA* 2.9 34.1 + - + +
274B GLU* 2.5 44.6 + - + +
275B MET* 3.8 23.8 - - + +
278B PHE* 3.6 55.4 - - + -
304B TYR* 4.0 11.0 + - - -
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 3.6 23.1 - - + -
162B ARG* 3.6 31.8 + - + +
164B ILE* 4.5 15.0 - - + -
182B GLU* 4.6 10.5 - - + +
183B LEU* 5.3 3.1 - - + -
220B ARG* 3.6 38.4 - - - +
262B MET 2.8 16.7 + - - +
263B THR* 3.5 9.0 - - - +
265B LYS* 1.3 78.0 - - - +
267B ALA* 1.3 60.2 + - - +
269B ASN* 3.1 16.6 + - - +
270B ALA 4.9 0.9 - - - +
275B MET* 3.7 20.1 - - + +
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.5 40.5 - - + +
2B VAL* 4.4 11.1 + - + +
4B ILE* 4.1 8.7 - - + -
133B ILE* 3.6 20.8 - - + +
162B ARG* 5.3 1.7 + - - +
263B THR 2.9 13.8 + - - +
264B LEU 3.4 10.1 - - - +
265B LYS 3.2 0.2 - - - -
266B LEU* 1.3 76.7 - - - +
268B GLU* 1.3 59.7 + - - +
269B ASN* 3.2 4.8 + - - -
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.6 27.1 - - + +
264B LEU* 3.1 25.8 + - - +
265B LYS* 3.1 36.4 + - - +
267B ALA* 1.3 75.6 - - - +
269B ASN* 1.3 69.7 + - - +
270B ALA* 3.3 4.8 + - + +
274B GLU* 4.5 1.9 - - - +
278B PHE* 6.1 0.5 - - - -
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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