Contacts of the helix formed by residues 347 - 364 (chain B) in PDB entry 1V40
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 THR 347 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ASP 4.9 1.1 - - - +
277B LEU* 3.3 21.5 - - - +
279B GLY* 4.2 15.7 - - - +
288B VAL* 3.7 23.5 - - + +
342B ILE* 4.0 15.4 - - + +
345B SER* 3.7 10.8 - - - +
346B VAL* 1.3 85.7 - - - +
348B TRP* 1.3 60.9 + - - +
349B ALA* 2.9 25.9 + - - +
350B ASP* 2.9 27.6 + - - +
351B PHE* 3.5 2.9 + - - -
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Residues in contact with TRP 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 3.8 16.8 - - + +
221B ILE* 4.4 7.6 - - + -
265B LEU* 4.0 24.0 - - + -
268B ALA* 3.6 25.1 - - + -
269B ARG* 4.1 24.4 - - + +
272B THR* 3.5 37.4 + - + -
277B LEU* 3.0 37.9 + - + +
278B ALA* 4.5 4.8 + - - +
288B VAL* 3.4 23.0 - - + +
289B ASP* 3.7 20.3 + - - -
292B VAL* 3.8 34.1 - - + -
347B THR* 1.3 71.6 - - - +
349B ALA* 1.3 57.3 + - - +
351B PHE* 3.3 17.5 - - + +
352B TYR* 2.9 28.3 + + + +
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B VAL* 3.9 21.5 - - + +
291B ILE* 4.3 8.5 - - + -
292B VAL* 4.0 14.1 - - + -
295B LEU* 4.6 2.9 - - - +
341B LEU* 3.9 5.0 - - + +
342B ILE* 3.8 23.1 - - + -
347B THR* 2.9 14.2 + - - +
348B TRP* 1.3 79.0 - - - +
350B ASP* 1.3 60.6 + - - +
352B TYR* 3.2 3.5 + - - +
353B TRP* 2.9 28.1 + - - +
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Residues in contact with ASP 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B TRP* 3.6 16.8 - - + +
341B LEU* 2.8 41.4 + - - +
342B ILE 4.9 0.2 + - - -
345B SER 4.3 0.2 - - - +
346B VAL* 3.4 13.4 - - + -
347B THR* 2.9 35.7 + - - +
349B ALA* 1.3 72.9 - - - +
351B PHE* 1.3 66.7 + - - +
353B TRP* 3.1 4.6 + - - +
354B GLU 3.0 18.2 + - - -
377B LEU* 3.7 9.5 - - + +
381B VAL* 3.7 26.5 - - + +
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Residues in contact with PHE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 3.7 9.9 - - + -
220B TYR* 3.9 33.2 - + + -
221B ILE* 4.5 8.1 - - + -
224B TYR* 3.7 35.2 - + + -
277B LEU* 3.8 25.4 - - + -
346B VAL* 3.8 21.3 - - + -
347B THR 3.5 4.9 + - - -
348B TRP* 3.3 19.7 + - - +
350B ASP* 1.3 80.2 - - - +
352B TYR* 1.3 60.9 + - - +
354B GLU* 3.3 4.5 + - - +
355B ILE* 3.0 29.2 + - - +
381B VAL* 3.8 17.9 - - + -
384B ILE* 3.9 14.6 - - + -
387B VAL* 3.9 13.0 - - + -
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Residues in contact with TYR 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 4.8 5.1 + - - +
217B ILE* 3.8 35.8 - - + +
264B SER* 5.2 1.6 + - - -
265B LEU* 4.0 18.4 - - + +
292B VAL* 3.5 44.2 - - + -
295B LEU* 3.9 11.2 - - + -
296B ASP* 2.8 31.4 + - + -
348B TRP* 2.9 14.7 + - + +
349B ALA 3.2 9.2 + - - +
351B PHE* 1.3 77.4 - - - +
353B TRP* 1.3 57.6 + - - +
355B ILE* 3.3 6.4 + - + +
356B CYS* 2.8 58.6 + - - -
3401B O16 3.2 21.0 - + - -
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Residues in contact with TRP 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.8 26.8 - - + +
328B MET* 3.5 31.4 - - + -
331B LEU* 3.7 22.9 - - + -
341B LEU* 3.9 15.3 - - + -
349B ALA 2.9 13.5 + - - +
350B ASP 3.4 7.6 - - - +
352B TYR* 1.3 76.2 - - - +
354B GLU* 1.3 53.8 + - + +
356B CYS* 4.8 0.7 - - + -
357B SER* 2.7 64.5 + - - -
360B LEU* 5.3 2.5 - - + -
367B LEU* 5.3 0.2 - - + -
368B LEU* 4.2 11.0 - - + -
374B LEU* 3.2 49.4 + - + +
377B LEU* 3.5 31.2 - - + +
378B ARG* 3.6 9.0 - - + +
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 2.7 33.8 + - - -
350B ASP 3.0 12.5 + - - +
351B PHE 3.7 6.1 - - - +
353B TRP* 1.3 76.6 - - - +
355B ILE* 1.3 61.4 + - - +
357B SER* 3.0 6.7 + - - -
358B THR* 2.8 44.7 + - - -
378B ARG* 3.2 20.8 + - - +
381B VAL* 3.9 17.0 - - + -
382B GLN* 2.6 47.4 + - + +
391B ILE* 4.4 3.4 - - - +
394B ARG* 5.2 2.6 + - - -
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Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG* 5.4 5.2 + - + +
213B GLY 4.4 2.5 - - - +
216B GLU* 3.7 22.0 - - + -
217B ILE* 3.3 44.4 - - + +
220B TYR* 3.7 34.1 - - + +
351B PHE 3.0 18.2 + - - +
352B TYR* 3.6 8.3 - - + +
354B GLU* 1.3 76.7 - - - +
356B CYS* 1.3 65.8 + - - +
358B THR* 3.3 14.0 + - - +
359B THR* 3.4 15.9 + - - +
3401B O16 4.2 21.1 - - + -
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Residues in contact with CYS 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.1 17.0 - - + -
299B MET* 3.6 28.0 - - + +
352B TYR* 2.8 46.3 + - - +
353B TRP* 4.1 4.9 - - + +
355B ILE* 1.3 73.8 - - - +
357B SER* 1.3 63.0 + - - +
359B THR* 3.3 5.5 + - - -
360B LEU* 3.0 30.1 + - + +
3401B O16 3.4 26.5 - - - -
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B TRP* 2.7 55.6 + - - -
354B GLU* 3.0 4.0 + - - -
356B CYS* 1.3 73.8 - - - +
358B THR* 1.3 65.0 + - - +
360B LEU* 3.8 8.8 - - - +
361B LEU* 2.9 29.7 + - - +
367B LEU* 5.2 2.0 - - - -
368B LEU* 4.7 4.5 - - - -
378B ARG* 2.7 35.8 + - - +
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Residues in contact with THR 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG* 3.7 29.4 - - - +
220B TYR* 5.3 0.4 + - - -
354B GLU* 2.8 42.9 + - - -
355B ILE* 3.5 8.1 - - - -
356B CYS 3.2 0.4 - - - -
357B SER* 1.3 78.8 + - - +
359B THR* 1.3 61.3 + - - +
361B LEU* 3.3 13.0 + - - +
362B VAL* 3.5 15.4 + - + +
378B ARG* 3.2 13.8 + - - +
382B GLN* 4.5 0.3 + - - -
394B ARG* 4.7 11.5 + - - +
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Residues in contact with THR 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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212B ARG* 3.4 23.6 + - - +
213B GLY 5.6 0.5 + - - -
299B MET* 4.0 13.0 - - + -
304B TRP* 3.9 29.6 - - + -
355B ILE* 3.4 8.6 + - - +
356B CYS 3.3 8.7 + - - -
358B THR* 1.3 80.1 - - - +
360B LEU* 1.3 62.1 + - - +
362B VAL* 3.1 21.7 + - + +
363B PHE* 3.2 14.5 - - + -
399B LEU* 4.5 16.5 + - + -
3401B O16 4.7 11.7 - - + -
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Residues in contact with LEU 360 (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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295B LEU* 6.4 1.1 - - + -
298B PHE* 4.0 20.0 - - + -
299B MET* 3.8 25.1 - - + -
302B PHE* 3.9 27.4 - - + -
304B TRP* 6.0 1.6 - - + -
320B LEU* 4.2 11.4 - - + +
328B MET* 4.2 13.9 - - + -
353B TRP* 5.3 2.0 - - + -
356B CYS* 3.0 25.0 + - + +
357B SER* 3.8 5.6 - - - +
359B THR* 1.3 77.1 - - + +
361B LEU* 1.3 57.4 + - - +
363B PHE* 3.2 9.4 + - + +
364B LYS* 2.9 29.5 + - - +
367B LEU* 3.6 28.9 - - + -
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Residues in contact with LEU 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 SER 2.9 20.9 + - - +
358B THR* 3.6 6.7 - - - +
359B THR 3.2 0.2 - - - -
360B LEU* 1.3 75.3 - - - +
362B VAL* 1.3 64.1 + - - +
363B PHE 3.2 0.2 - - - -
364B LYS 3.7 15.9 - - - +
365B PRO* 3.3 40.0 - - + +
367B LEU* 4.0 15.7 - - + -
368B LEU* 4.4 19.3 - - + +
378B ARG* 3.2 43.5 - - - +
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG* 4.7 3.4 - - - +
358B THR* 3.5 16.6 - - + +
359B THR* 3.1 14.7 + - + +
361B LEU* 1.3 80.0 - - - +
363B PHE* 1.3 70.0 + - + +
365B PRO* 4.6 5.4 - - - +
398B LYS* 3.9 48.2 - - + +
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 6.0 1.1 - + - -
304B TRP* 3.9 15.9 - + - -
316B PHE* 3.9 25.1 - + + -
320B LEU* 4.3 21.1 - - + +
359B THR* 3.2 37.2 - - + -
360B LEU* 3.2 8.7 + - + +
362B VAL* 1.3 90.4 - - + +
364B LYS* 1.3 58.0 + - - +
365B PRO* 3.7 6.8 - - - +
398B LYS* 4.5 19.3 - - - -
399B LEU* 3.6 24.9 - - + -
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Residues in contact with LYS 364 (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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320B LEU* 2.7 52.2 + - + +
321B THR* 3.8 8.7 + - - +
325B PRO* 3.6 20.2 - - - +
360B LEU 2.9 10.4 + - - +
361B LEU* 3.5 9.9 - - - -
363B PHE* 1.3 79.9 - - - +
365B PRO* 1.3 58.6 - - - +
366B ASP* 3.1 27.8 - - - +
367B LEU* 3.0 47.0 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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