Contacts of the helix formed by residues 346 - 364 (chain B) in PDB entry 4D10
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 HIS 346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B LEU* 3.6 37.8 + - + +
251B PHE* 4.5 8.4 - + - -
282B LEU* 4.5 8.3 - - + -
286B LEU* 3.8 32.6 - - + +
342B PHE* 3.2 24.9 - - - +
343B ILE 3.3 6.4 + - - +
345B GLU* 1.3 100.4 + - + +
347B ILE* 1.3 58.9 + - - +
348B GLU 3.3 2.7 - - - -
349B GLU* 3.3 23.8 + - - +
350B LEU* 3.0 28.2 + - - +
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Residues in contact with ILE 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 5.7 0.4 - - + -
285B MET* 6.2 1.1 - - + -
314B LEU* 5.3 3.4 - - + -
326B PHE* 4.1 20.8 - - + -
330B LEU* 3.8 40.4 - - + -
337B ILE* 4.5 11.0 - - + -
338B MET* 4.2 18.8 - - + -
343B ILE* 3.0 20.4 + - + +
344B ARG* 3.4 23.1 - - - +
345B GLU 3.6 0.2 - - - -
346B HIS* 1.3 77.3 - - - +
348B GLU* 1.3 62.3 + - + +
350B LEU* 3.7 11.2 - - + +
351B LEU* 2.9 28.2 + - - +
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG 4.7 1.5 + - - +
345B GLU 5.2 5.4 - - - +
346B HIS 3.3 0.8 - - - -
347B ILE* 1.3 81.1 - - + +
349B GLU* 1.3 61.0 + - - +
351B LEU* 3.4 21.1 + - - +
352B ARG* 3.0 68.9 + - - +
355B ARG* 5.4 0.9 + - - -
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Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 3.9 18.1 - - - -
286B LEU* 3.9 18.9 - - + +
288B LYS* 6.1 0.2 - - - +
345B GLU 5.2 1.7 + - - +
346B HIS* 3.3 32.0 + - - +
348B GLU* 1.3 76.9 - - - +
350B LEU* 1.3 57.4 + - - +
352B ARG* 3.4 9.3 + - - +
353B ASN* 2.9 43.1 + - - +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 4.7 10.3 - - + -
285B MET* 3.7 58.8 - - + +
286B LEU* 3.7 22.9 - - + +
318B TYR* 3.7 16.8 - - + +
326B PHE* 3.7 24.0 - - + -
346B HIS 3.0 15.0 + - - +
347B ILE* 3.7 15.0 - - + +
349B GLU* 1.3 73.5 - - - +
351B LEU* 1.3 65.5 + - - +
353B ASN* 3.1 10.2 + - - +
354B ILE* 3.1 27.4 + - - +
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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
----------------------------------------------------------
323B ILE* 4.8 6.0 - - + +
326B PHE* 3.7 27.3 - - + -
327B GLU* 4.1 23.8 - - + +
330B LEU* 4.4 7.9 - - + -
347B ILE* 2.9 17.8 + - + +
348B GLU* 3.5 24.5 - - - +
350B LEU* 1.3 76.1 - - - +
352B ARG* 1.3 57.5 + - - +
354B ILE* 3.2 10.7 + - + +
355B ARG* 3.0 62.7 + - - +
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Residues in contact with ARG 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLU* 3.0 50.8 + - - +
349B GLU* 3.7 7.6 - - - +
350B LEU 3.3 0.2 - - - -
351B LEU* 1.3 76.0 - - - +
353B ASN* 1.3 55.2 + - - +
355B ARG* 3.4 15.0 + - - +
356B THR* 2.7 38.5 + - - +
384B ASP* 5.8 3.2 + - - -
388B LEU* 4.6 19.8 - - + +
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Residues in contact with ASN 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 5.1 2.8 + - - +
288B LYS* 3.1 44.2 + - - +
318B TYR* 3.8 20.2 + - - +
349B GLU* 2.9 43.3 + - - +
350B LEU* 3.1 16.9 + - - +
352B ARG* 1.3 78.4 - - - +
354B ILE* 1.3 60.2 + - - +
356B THR* 3.8 8.1 + - - -
357B GLN* 3.8 15.4 + - - +
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA 5.1 0.2 - - - +
318B TYR* 3.6 22.7 - - + +
321B ASN* 3.8 15.0 - - - +
322B ASP 3.8 28.0 - - - +
323B ILE* 3.8 18.2 - - + -
326B PHE* 3.6 49.6 - - + -
350B LEU 3.1 18.7 + - - +
351B LEU* 3.2 10.1 + - + +
353B ASN* 1.3 73.7 - - - +
355B ARG* 1.3 66.6 + - - +
357B GLN* 3.1 8.3 + - - +
358B VAL* 3.0 25.6 + - + +
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Residues in contact with ARG 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ILE* 3.9 27.0 - - + +
327B GLU* 3.0 29.7 + - - -
348B GLU* 5.4 0.8 + - - -
351B LEU* 3.0 44.3 + - - +
352B ARG* 3.6 17.7 - - - +
354B ILE* 1.3 77.6 - - - +
356B THR* 1.3 55.9 + - - +
358B VAL* 3.9 1.3 - - - +
359B LEU* 3.0 30.7 + - - +
378B LEU* 2.7 38.3 + - + +
379B ASN 3.5 13.9 + - - -
380B ILE* 3.5 36.1 - - - +
388B LEU* 4.6 13.5 - - + -
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Residues in contact with THR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LYS* 6.0 5.6 - - - +
352B ARG* 2.7 22.7 + - - +
353B ASN* 3.9 10.1 + - - -
354B ILE 3.2 0.2 - - - -
355B ARG* 1.3 76.3 - - - +
357B GLN* 1.3 58.0 + - - +
359B LEU* 3.4 7.1 + - - +
360B ILE* 3.0 46.9 + - + +
388B LEU* 4.2 12.5 - - - +
391B GLN* 5.1 1.4 + - - -
392B CYS* 3.6 29.0 - - - -
397B THR* 4.7 9.0 - - + +
398B ILE* 5.3 0.4 - - + +
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Residues in contact with GLN 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ASN* 3.6 34.5 - - - +
353B ASN 3.8 8.4 + - - +
354B ILE 3.1 7.7 + - - +
356B THR* 1.3 76.7 - - - +
358B VAL* 1.3 60.2 + - - +
360B ILE* 3.2 30.7 + - - +
361B LYS* 2.9 28.4 + - - +
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ASN* 3.5 31.6 - - + +
323B ILE* 3.8 28.9 - - + +
354B ILE* 3.0 16.3 + - + +
355B ARG 4.0 1.3 - - - +
357B GLN* 1.3 75.7 - - - +
359B LEU* 1.3 58.2 + - - +
361B LYS* 3.3 10.8 + - + +
362B LEU* 3.0 29.1 + - + +
377B GLU* 6.0 2.0 - - + +
378B LEU* 3.8 17.0 - - + -
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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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355B ARG 3.0 17.6 + - - +
356B THR* 3.5 5.4 - - - +
358B VAL* 1.3 73.9 - - - +
360B ILE* 1.3 54.5 + - - +
362B LEU* 3.0 9.8 + - + +
363B ILE* 2.8 52.9 + - + +
374B ILE* 3.7 35.2 - - + -
378B LEU* 4.1 11.7 - - + +
385B VAL* 5.9 0.9 - - + -
388B LEU* 3.8 26.7 - - + -
389B LEU* 3.9 17.9 - - + +
392B CYS* 5.2 0.7 - - - -
398B ILE* 3.6 28.0 - - + -
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Residues in contact with ILE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 3.0 38.9 + - + +
357B GLN* 3.2 31.4 + - - +
359B LEU* 1.3 74.6 - - - +
361B LYS* 1.3 60.6 - - - +
363B ILE* 3.4 22.5 - - + +
364B LYS* 3.6 12.5 + - - +
397B THR* 4.3 22.2 - - + +
398B ILE* 4.0 20.2 - - + -
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Residues in contact with LYS 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 GLN* 2.9 15.4 + - - +
358B VAL* 3.6 13.9 - - + +
359B LEU 3.3 0.2 - - - -
360B ILE* 1.3 75.9 - - - +
362B LEU* 1.3 59.7 + - - +
364B LYS* 4.2 13.4 + - - +
365B PRO* 4.2 4.7 - - - +
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Residues in contact with LEU 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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358B VAL* 3.0 16.5 + - + +
359B LEU* 3.0 14.1 + - + +
361B LYS* 1.3 77.9 - - - +
363B ILE* 1.3 59.7 + - - +
364B LYS 3.4 0.4 - - - -
365B PRO* 3.4 5.3 - - - +
366B TYR* 3.2 29.2 - - + -
369B ILE* 4.2 3.7 - - + +
373B PHE* 4.1 17.9 - - + -
374B ILE* 4.1 31.4 - - + -
377B GLU* 3.8 41.5 - - + +
378B LEU* 5.2 5.2 - - + -
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Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 2.8 42.8 + - + +
360B ILE* 3.4 19.7 - - + +
362B LEU* 1.3 73.8 - - - +
364B LYS* 1.3 65.7 + - - +
365B PRO 3.5 0.4 - - - -
366B TYR* 3.2 23.3 + - - +
369B ILE* 4.4 9.9 - - + -
374B ILE* 5.0 0.4 - - + -
397B THR 5.7 0.2 - - - +
398B ILE* 3.9 29.4 - - + -
399B HIS 5.1 1.8 - - - +
409B LEU* 3.8 25.6 - - + -
411B LEU* 3.4 34.5 - - + +
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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
----------------------------------------------------------
360B ILE 3.6 11.8 + - - +
361B LYS* 4.2 8.5 - - - +
362B LEU 3.4 0.4 - - - -
363B ILE* 1.3 81.8 - - - +
365B PRO* 1.4 66.7 - - + +
366B TYR 3.6 3.5 + - - +
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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
------------------------------------------------------------
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