Contacts of the helix formed by residues 349 - 363 (chain B) in PDB entry 3CUQ
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 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B GLU* 4.0 20.5 + - - -
343B ALA* 4.1 0.2 - - - -
348B MET* 1.3 78.5 - - - +
350B VAL* 1.3 66.2 + - - +
351B LEU* 3.9 7.8 + - - +
352B LEU* 3.2 24.3 + - - +
353B ALA* 3.1 19.2 + - - +
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Residues in contact with VAL 350 (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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112A LYS* 4.9 18.3 - - - +
339B SER* 4.7 6.7 - - - -
340B GLU* 3.8 44.6 - - + +
343B ALA* 3.9 20.2 - - + -
348B MET 3.7 0.2 + - - -
349B SER* 1.3 71.7 - - - +
351B LEU* 1.3 64.2 + - - +
353B ALA* 3.2 3.3 + - - +
354B LYS* 2.9 24.3 + - + +
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Residues in contact with LEU 351 (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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156A THR 5.8 0.7 - - - +
173A PRO* 3.5 38.1 - - + -
265B SER* 3.9 28.9 - - - +
267B THR* 5.7 4.3 - - + -
268B GLU* 5.6 1.6 - - - +
310B VAL* 4.0 22.7 - - + -
349B SER* 4.1 6.9 - - - +
350B VAL* 1.3 77.6 - - - +
352B LEU* 1.3 72.2 + - + +
354B LYS* 3.2 16.4 + - - +
355B GLU* 3.3 21.1 + - + +
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE* 3.7 45.5 - - + +
264B MET* 5.5 0.7 - - - -
265B SER* 4.4 9.4 - - - +
268B GLU* 5.3 2.0 - - - +
306B PHE* 4.6 13.0 - - + -
310B VAL* 5.2 1.8 - - + -
312B VAL* 4.1 19.5 - - + -
320B GLU* 4.6 5.3 - - - +
348B MET* 3.4 21.4 - - + +
349B SER* 3.2 18.8 + - - +
351B LEU* 1.3 103.3 - - + +
353B ALA* 1.3 57.0 + - - +
355B GLU* 3.5 7.0 + - + +
356B ARG* 3.0 27.4 + - - +
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Residues in contact with ALA 353 (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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339B SER* 3.9 16.6 - - - +
342B PHE* 3.7 24.0 - - + -
343B ALA* 4.0 7.9 - - + -
348B MET* 3.9 12.1 - - + +
349B SER 3.1 12.9 + - - +
350B VAL 3.5 8.1 - - - +
352B LEU* 1.3 77.0 - - - +
354B LYS* 1.3 66.0 + - - +
356B ARG* 3.2 5.5 + - - +
357B LEU* 3.1 28.1 + - - +
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Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PRO* 6.6 0.4 - - - -
219A GLU* 5.1 13.8 + - - -
339B SER* 3.4 26.2 + - - +
350B VAL* 2.9 14.8 + - + +
351B LEU* 3.5 11.0 - - - +
353B ALA* 1.3 74.7 - - - +
355B GLU* 1.3 68.2 + - - +
357B LEU* 3.0 6.1 + - - +
358B LEU* 3.0 52.7 + - + +
375B LEU* 4.5 19.6 - - - +
377B PHE* 5.5 2.0 - - + -
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Residues in contact with GLU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PHE* 3.9 50.8 - - + +
308B SER* 2.8 35.9 + - - -
310B VAL* 4.4 10.2 - - + +
320B GLU* 5.5 2.5 - - + +
351B LEU* 3.3 15.9 + - + +
352B LEU* 3.7 11.0 - - + +
353B ALA 3.3 0.4 - - - -
354B LYS* 1.3 82.4 - - - +
356B ARG* 1.3 64.1 + - - +
358B LEU* 3.3 17.7 + - - +
359B LEU* 3.0 26.1 + - - +
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Residues in contact with ARG 356 (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 GLY 5.8 0.2 + - - -
263B ILE* 4.9 3.0 - - - +
318B HIS* 4.3 4.6 - - - -
320B GLU* 2.6 53.7 + - - +
323B MET* 3.5 41.8 + - - +
324B VAL* 4.5 4.8 - - + +
326B SER* 5.0 4.9 + - - -
327B ALA* 4.2 18.9 - - + +
342B PHE* 4.7 12.7 - - + -
346B VAL* 5.1 10.1 - - - +
348B MET* 3.4 34.0 - - - +
352B LEU 3.0 17.2 + - - +
353B ALA* 3.2 8.7 + - - +
355B GLU* 1.3 78.7 - - - +
357B LEU* 1.3 61.0 + - - +
359B LEU* 3.5 6.5 + - - +
360B ALA* 3.2 20.1 + - - +
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Residues in contact with LEU 357 (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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327B ALA* 4.3 8.3 - - + -
331B VAL* 4.1 15.9 - - + -
337B LEU* 4.3 2.9 - - + -
338B THR 4.3 2.2 - - - +
339B SER* 4.0 23.1 - - - +
342B PHE* 4.1 35.0 - - + -
353B ALA 3.1 15.3 + - - +
354B LYS* 3.0 4.5 + - - +
356B ARG* 1.3 75.4 - - - +
358B LEU* 1.3 65.2 + - - +
359B LEU 3.0 1.8 - - - -
360B ALA* 3.1 2.8 + - - +
361B GLU* 3.0 22.9 + - - +
366B LEU* 3.5 27.9 - - + +
377B PHE* 3.5 38.6 - - + -
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Residues in contact with LEU 358 (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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308B SER* 6.3 1.1 - - - -
354B LYS* 3.0 44.3 + - + +
355B GLU* 3.7 19.5 - - - +
357B LEU* 1.3 76.3 - - - +
359B LEU* 1.3 58.7 + - - +
361B GLU* 3.4 12.1 - - - +
362B LYS* 2.9 37.4 + - + +
368B ARG* 3.4 29.2 - - - +
375B LEU* 5.4 2.0 - - + -
377B PHE* 4.2 12.3 - - + -
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Residues in contact with LEU 359 (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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304B ARG* 5.9 0.7 - - - +
306B PHE* 6.3 1.8 - - + -
320B GLU* 3.8 34.1 - - + +
321B GLU* 3.9 13.5 - - + +
324B VAL* 3.7 22.2 - - + -
355B GLU 3.0 17.4 + - - +
356B ARG* 3.7 4.9 - - - +
357B LEU 3.0 0.2 - - - -
358B LEU* 1.3 78.2 - - - +
360B ALA* 1.3 59.9 + - - +
362B LYS* 3.2 26.5 + - + +
363B MET* 3.0 46.7 + - + +
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 3.7 34.5 - - + +
327B ALA* 5.0 3.4 - - + -
328B LEU* 5.8 0.7 - - + +
356B ARG 3.2 11.0 + - - +
357B LEU* 3.1 3.0 + - - +
359B LEU* 1.3 82.1 - - - +
361B GLU* 1.3 54.7 + - - +
363B MET* 3.4 2.1 + - - +
364B GLY 3.3 2.9 + - - -
365B HIS* 2.7 36.2 + - + +
366B LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 361 (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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357B LEU 3.0 12.1 + - - +
358B LEU* 3.4 19.5 - - - +
360B ALA* 1.3 73.5 - - - +
362B LYS* 1.3 58.2 + - - +
363B MET 3.0 1.3 - - - -
364B GLY* 2.7 22.5 + - - -
366B LEU* 3.4 27.0 - - + +
367B CYS* 4.6 3.1 - - - -
368B ARG* 2.5 55.7 + - - +
377B PHE* 4.1 11.7 - - + -
20D GLN* 4.3 1.6 - - - +
21D PRO* 3.3 18.3 - - - +
22D ASN* 3.1 19.8 + - + +
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Residues in contact with LYS 362 (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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307B ASP* 3.8 20.5 + - - -
358B LEU* 2.9 27.3 + - + +
359B LEU* 3.2 29.8 + - + +
361B GLU* 1.3 72.3 + - - +
363B MET* 1.3 58.2 + - + +
22D ASN* 3.3 17.3 + - - +
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Residues in contact with MET 363 (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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321B GLU* 4.0 22.4 - - + +
324B VAL* 3.8 37.2 - - + -
359B LEU* 3.0 34.2 + - + +
360B ALA* 3.9 5.2 - - - +
361B GLU 3.0 1.0 - - - -
362B LYS* 1.3 78.5 - - + +
364B GLY* 1.3 62.6 + - - +
365B HIS* 3.3 25.2 + - + +
22D ASN* 4.3 0.7 - - - -
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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