Contacts of the helix formed by residues 329 - 340 (chain B) in PDB entry 4UFT
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 TYR 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268B SER 2.7 28.3 + - - -
269B PHE* 4.2 6.2 - - - -
272B THR* 4.5 9.2 - - + -
292B GLU* 3.7 30.7 - - + +
295B THR* 5.1 8.3 - - + -
296B LEU* 3.9 24.4 - - + +
299B LEU* 3.6 27.6 - - + +
323B LYS 4.3 1.8 - - - -
324B PHE 3.3 9.5 + - - -
325B SER 3.4 19.3 - - - -
326B ALA* 3.2 8.7 + - + -
328B SER* 1.3 89.8 - - - +
330B PRO* 1.3 63.8 - - - +
331B LEU 3.3 2.7 - - - -
332B LEU* 4.3 8.1 - - + -
333B TRP* 3.3 32.5 + - + +
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Residues in contact with PRO 330 (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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292B GLU* 5.0 2.9 - - - +
326B ALA 3.1 5.6 - - - +
327B GLY 3.5 15.3 - - - +
328B SER 3.6 3.8 - - - +
329B TYR* 1.3 87.6 - - - +
331B LEU* 1.3 78.2 + - + +
333B TRP* 4.1 7.3 - - + -
334B SER* 3.1 28.6 + - - -
356B TYR* 3.7 40.1 - - + +
358B ASP* 4.4 6.5 - - + +
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Residues in contact with LEU 331 (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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288B GLU* 3.8 43.1 - - + +
289B PHE* 3.4 18.9 - - + -
292B GLU* 4.0 22.2 - - - +
329B TYR 3.3 0.8 - - - -
330B PRO* 1.3 91.3 - - + +
332B LEU* 1.3 65.0 + - - +
334B SER* 2.7 21.1 + - - -
335B TYR 3.3 5.7 + - - -
358B ASP* 4.1 14.5 - - - +
361B TYR* 4.8 10.8 - - + +
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Residues in contact with LEU 332 (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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272B THR* 3.4 24.0 - - - +
276B GLY* 5.8 1.3 - - - -
277B ILE* 4.7 10.3 - - + -
284B LEU* 4.4 21.3 - - + -
289B PHE* 3.8 25.1 - - + +
292B GLU* 3.7 28.4 - - + +
293B LEU* 5.1 5.8 - - + +
296B LEU* 3.9 26.9 - - + -
329B TYR* 3.8 12.5 + - + +
331B LEU* 1.3 79.3 - - - +
333B TRP* 1.3 58.6 + - - +
335B TYR* 3.4 5.7 + - + +
336B ALA* 3.0 29.4 + - + +
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Residues in contact with TRP 333 (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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267B ALA 5.2 0.8 + - - -
268B SER* 3.4 34.4 - - - +
272B THR* 4.1 17.7 - - - -
326B ALA* 3.7 20.4 - - + -
329B TYR* 3.3 25.4 + + + +
330B PRO* 4.1 8.1 - - + +
332B LEU* 1.3 81.0 - - - +
334B SER* 1.3 67.9 + - - +
336B ALA* 3.9 0.5 - - - +
337B MET* 3.0 72.3 + - + +
352B PHE* 6.2 0.2 - - + -
353B GLY 5.9 0.9 - - - -
354B ARG* 3.3 48.7 - - + -
356B TYR* 3.9 22.0 - + - -
357B PHE* 4.3 16.6 - + - -
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Residues in contact with SER 334 (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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330B PRO 3.1 14.8 + - - -
331B LEU 2.7 21.5 + - - -
333B TRP* 1.3 86.6 - - - +
335B TYR* 1.3 56.2 + - - +
337B MET* 4.7 2.7 - - - -
338B GLY 3.1 19.1 + - - -
357B PHE 3.4 24.9 - - - -
358B ASP* 3.1 24.4 + - - -
361B TYR* 3.9 4.9 - - - +
362B PHE* 3.6 22.6 - - - -
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Residues in contact with TYR 335 (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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276B GLY* 5.2 6.3 - - - -
281B TYR* 3.5 26.8 - + + +
283B ALA* 2.7 30.4 + - - +
284B LEU* 4.2 23.3 - - + -
289B PHE* 3.6 33.2 - + + -
331B LEU 3.3 1.3 + - - +
332B LEU* 3.8 7.2 - - + +
333B TRP 3.2 0.4 - - - -
334B SER* 1.3 79.6 + - - +
336B ALA* 1.3 63.3 + - + +
338B GLY* 5.0 0.4 - - - -
339B VAL* 2.8 46.7 + - + +
361B TYR* 4.1 10.3 - - + +
364B LEU* 3.7 22.4 - - + -
365B GLY* 3.7 26.9 - - - -
368B MET* 4.4 5.0 - - + +
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Residues in contact with ALA 336 (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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272B THR* 3.3 46.2 - - - +
275B PHE* 3.3 24.1 - - - +
276B GLY* 3.7 13.0 - - - +
332B LEU* 3.0 16.1 + - + +
333B TRP* 4.0 1.6 - - + +
335B TYR* 1.3 79.1 - - + +
337B MET* 1.3 61.0 + - - +
339B VAL* 3.4 8.3 - - - +
340B GLY* 3.4 8.5 + - - -
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Residues in contact with MET 337 (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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275B PHE* 5.6 2.9 - - - -
333B TRP* 3.0 64.4 + - + +
334B SER* 4.2 2.7 - - - +
336B ALA* 1.3 78.4 - - - +
338B GLY* 1.3 61.2 + - - +
340B GLY* 3.5 9.1 + - - +
341B VAL* 3.4 15.4 - - - +
347B MET* 5.4 8.8 - - + +
350B LEU* 4.7 8.1 - - + -
352B PHE* 3.5 35.4 - - + -
354B ARG* 5.4 0.2 - - - -
357B PHE* 3.8 27.1 - - + +
362B PHE* 3.8 15.3 - - + -
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Residues in contact with GLY 338 (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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334B SER 3.1 11.4 + - - -
335B TYR 3.7 2.0 - - - -
337B MET* 1.3 77.6 - - - +
339B VAL* 1.3 60.9 + - - +
341B VAL* 3.3 19.0 + - - +
342B GLU* 4.3 0.3 - - - +
362B PHE* 3.6 35.6 - - - -
365B GLY 4.1 0.2 - - - -
366B GLN* 3.6 22.0 + - - +
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PHE 3.6 21.1 - - - +
276B GLY* 4.8 0.4 - - - -
281B TYR* 3.6 32.1 - - + -
335B TYR* 2.8 40.7 + - + +
336B ALA* 3.4 13.2 - - - +
338B GLY* 1.3 72.8 - - - +
340B GLY* 1.3 59.4 + - - +
341B VAL 3.3 3.5 + - - -
342B GLU 4.5 1.4 + - - -
343B LEU* 3.3 17.4 - - - +
365B GLY* 3.4 29.7 - - - +
368B MET* 4.8 1.6 - - + -
369B VAL* 3.5 14.0 - - + +
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Residues in contact with GLY 340 (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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275B PHE* 3.7 31.5 - - - -
336B ALA 3.4 8.5 + - - -
337B MET 3.5 6.7 + - - -
338B GLY 3.2 1.4 - - - -
339B VAL* 1.3 82.1 - - - +
341B VAL* 1.3 58.4 + - - +
342B GLU 3.7 0.7 - - - -
343B LEU* 4.1 9.6 - - - -
344B GLU 4.3 3.3 + - - -
347B MET* 3.4 24.0 - - - +
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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