Contacts of the helix formed by residues 264 - 276 (chain B) in PDB entry 1U3Q
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 SER 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B ALA 3.5 2.5 + - - -
263B LEU* 1.3 76.7 - - - +
265B PRO* 1.3 77.9 - - - +
266B GLU* 3.7 6.7 + - - +
267B GLN* 2.9 40.9 + - - +
268B LEU* 2.9 21.4 + - - +
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Residues in contact with PRO 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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263B LEU 4.8 0.4 - - - +
264B SER* 1.3 87.1 - - - +
266B GLU* 1.3 62.5 + - - +
268B LEU* 3.1 7.7 + - + +
269B VAL* 3.0 28.7 + - - +
432B ALA 5.5 1.6 - - - +
435B ASP* 4.0 26.2 - - + +
436B ALA* 3.9 7.6 - - - +
439B TRP* 3.8 31.2 - - + -
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Residues in contact with GLU 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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264B SER* 3.3 6.5 + - - +
265B PRO* 1.3 80.9 - - - +
267B GLN* 1.3 66.1 + - + +
269B VAL* 3.2 4.5 + - - +
270B LEU* 3.2 40.7 + - + +
439B TRP* 3.6 45.3 + - + +
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Residues in contact with GLN 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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262B ALA 4.0 4.0 - - - +
263B LEU* 3.7 26.2 - - + +
264B SER* 2.9 41.0 + - - +
266B GLU* 1.3 81.0 - - + +
268B LEU* 1.3 62.0 + - - +
270B LEU* 3.4 11.5 + - + +
271B THR* 2.9 28.4 + - - -
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Residues in contact with LEU 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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263B LEU* 4.0 13.8 - - + +
264B SER 2.9 13.8 + - - +
265B PRO* 3.5 9.4 - - + +
267B GLN* 1.3 75.2 - - - +
269B VAL* 1.3 66.2 + - - +
271B THR* 3.0 13.1 + - - -
272B LEU* 3.0 25.8 + - + +
317B PRO* 3.3 41.1 - - + -
432B ALA* 3.4 44.4 - - + +
433B VAL* 3.7 18.2 - - + +
436B ALA* 4.0 7.2 - - + -
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Residues in contact with VAL 269 (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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265B PRO 3.0 15.6 + - - +
266B GLU 3.2 6.9 + - - +
268B LEU* 1.3 75.6 - - - +
270B LEU* 1.3 62.7 + - + +
272B LEU* 3.4 11.3 + - - +
273B LEU* 3.1 20.8 + - - +
395B LYS* 3.5 50.7 - - + +
398B LEU* 4.1 4.8 - - + +
399B CYS* 4.2 4.7 - - - -
436B ALA* 3.7 17.5 - - + -
439B TRP* 3.8 15.5 - - + -
440B VAL* 3.8 20.6 - - + -
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Residues in contact with LEU 270 (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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266B GLU* 3.2 35.1 + - + +
267B GLN* 3.8 10.8 - - + +
269B VAL* 1.3 79.0 - - + +
271B THR* 1.3 57.1 + - - +
273B LEU* 3.2 14.0 + - + +
274B GLU* 3.0 27.9 + - - +
395B LYS* 3.5 29.2 - - - +
439B TRP* 6.2 1.1 - - + -
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Residues in contact with THR 271 (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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263B LEU* 3.8 13.8 - - + +
267B GLN 2.9 18.4 + - - -
268B LEU* 3.0 12.8 + - - -
270B LEU* 1.3 74.3 - - - +
272B LEU* 1.3 61.9 + - + +
274B GLU* 3.2 10.4 + - + +
275B ALA* 3.0 26.4 + - + +
315B LYS* 3.8 21.3 - - + +
317B PRO* 4.2 16.2 - - + -
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Residues in contact with LEU 272 (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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268B LEU* 3.0 31.3 + - + +
269B VAL* 3.8 6.7 - - - +
271B THR* 1.3 74.7 - - - +
273B LEU* 1.3 62.2 + - - +
275B ALA* 3.2 7.1 + - + +
276B GLU* 3.0 23.9 + - - +
312B TRP* 5.1 8.5 + - - +
316B ILE* 3.7 38.4 - - + -
317B PRO* 4.8 4.5 - - + -
398B LEU* 3.8 34.7 - - + +
399B CYS* 4.1 18.4 - - - +
402B ALA* 4.1 20.4 - - + -
433B VAL* 4.7 5.4 - - + -
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Residues in contact with LEU 273 (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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269B VAL 3.1 13.9 + - - +
270B LEU* 3.4 17.3 - - + +
271B THR 3.1 0.2 - - - -
272B LEU* 1.3 79.3 - - - +
274B GLU* 1.3 61.7 + - - +
276B GLU* 3.3 18.0 + - + +
394B HIS* 4.0 28.7 - - + +
395B LYS* 4.2 25.8 - - - +
398B LEU* 3.5 15.0 - - + +
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Residues in contact with GLU 274 (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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270B LEU 3.0 12.7 + - - +
271B THR* 3.5 11.9 - - - +
273B LEU* 1.3 78.4 - - - +
275B ALA* 1.3 64.0 + - - +
276B GLU 3.4 4.9 + - - +
315B LYS* 4.0 21.9 - - - +
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Residues in contact with ALA 275 (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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271B THR 3.0 16.0 + - - +
272B LEU* 3.2 12.5 + - + +
274B GLU* 1.3 76.6 + - - +
276B GLU* 1.3 67.0 + - - +
277B PRO* 3.1 4.3 - - - +
312B TRP* 3.6 27.2 - - + +
315B LYS* 3.5 49.0 + - + +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU 3.0 6.7 + - - +
273B LEU* 3.5 16.6 - - + +
274B GLU 3.3 5.8 - - - +
275B ALA* 1.3 77.3 - - - +
277B PRO* 1.3 83.3 - - + +
278B PRO* 4.3 1.4 - - - +
312B TRP* 4.1 5.5 + - - -
394B HIS* 4.6 13.4 + - + +
397B TYR* 3.6 16.3 + - - -
398B LEU* 3.4 29.6 - - + +
401B LYS* 2.7 33.9 + - - -
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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