Contacts of the helix formed by residues 341 - 359 (chain B) in PDB entry 1JGG
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 PRO 341 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306B THR* 5.6 1.6 - - - +
335B ALA* 4.2 0.7 - - - -
339B ASN 4.5 1.8 - - - +
340B LEU* 1.3 96.2 - - + +
342B GLU* 1.3 65.3 + - - +
343B SER* 3.8 12.6 - - - +
344B THR* 3.0 39.4 + - + +
345B ILE* 3.3 11.8 + - - +
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Residues in contact with GLU 342 (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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328B ARG 5.8 0.9 - - - +
331B ARG* 4.6 17.6 + - + +
332B CYS* 3.7 30.3 - - - -
335B ALA* 4.1 15.2 - - + +
340B LEU 3.9 1.6 + - - -
341B PRO* 1.3 70.9 - - - +
343B SER* 1.3 65.3 + - - +
345B ILE* 3.3 4.8 + - - +
346B LYS* 3.1 21.6 + - + +
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Residues in contact with SER 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PRO* 3.8 12.6 - - - +
342B GLU* 1.3 80.3 - - - +
344B THR* 1.3 65.7 + - - -
346B LYS* 3.5 11.6 - - - +
347B VAL* 2.9 33.1 + - - +
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Residues in contact with THR 344 (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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306B THR* 4.2 14.5 + - + -
308B PHE* 3.9 26.9 - - + -
340B LEU* 4.0 21.1 - - + -
341B PRO* 3.0 33.0 + - - +
343B SER* 1.3 79.7 + - - +
345B ILE* 1.3 59.4 + - - +
347B VAL* 3.4 4.0 + - - +
348B TRP* 2.9 28.1 + - - +
203C A 4.3 19.6 + - - +
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Residues in contact with ILE 345 (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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316B LEU* 4.5 16.8 - - + -
331B ARG* 4.1 25.8 - - + +
334B LEU* 4.4 10.5 - - + +
335B ALA* 3.6 35.4 - - + +
338B LEU* 5.0 1.6 - - + -
340B LEU* 3.8 29.6 - - + -
341B PRO 3.3 20.1 + - - +
342B GLU 3.8 4.9 - - - +
343B SER 3.3 0.4 - - - -
344B THR* 1.3 74.8 - - - +
346B LYS* 1.3 66.1 + - - +
348B TRP* 3.0 16.1 + - - +
349B PHE* 3.1 36.3 + - + -
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Residues in contact with LYS 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ARG* 6.0 0.9 - - - +
331B ARG* 3.5 45.7 - - - +
342B GLU* 3.1 12.8 + - + +
343B SER* 3.2 13.7 + - - +
345B ILE* 1.3 77.9 - - - +
347B VAL* 1.3 77.5 + - - +
349B PHE* 3.3 4.6 + - - +
350B GLN* 3.1 21.0 + - + +
353B ARG* 5.4 0.9 + - - -
214D T 5.7 6.1 - - - +
215D C 5.6 5.9 - - - +
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B SER* 2.9 22.6 + - - +
344B THR* 3.8 3.4 - - - +
346B LYS* 1.3 88.5 - - - +
348B TRP* 1.3 66.1 + - - +
350B GLN* 3.1 12.8 - - - +
351B ASN* 2.9 38.9 + - - +
202C A 4.8 0.9 - - + -
203C A 3.8 23.8 - - + +
204C T 3.7 33.2 - - + +
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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
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308B PHE* 4.0 23.6 - + + -
313B LEU* 3.7 18.6 - - + +
316B LEU* 3.5 60.1 - - + +
317B GLU* 3.4 23.3 - - - -
320B PHE* 4.0 9.9 - + + -
344B THR 2.9 17.6 + - - +
345B ILE* 3.0 5.1 + - - +
347B VAL* 1.3 77.7 - - - +
349B PHE* 1.3 81.7 + + - +
351B ASN* 3.0 6.7 + - - +
352B ARG* 2.8 62.2 + - + +
202C A 3.6 26.1 + - - -
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Residues in contact with PHE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 4.0 12.3 - - + -
319B GLU* 3.6 29.8 - - + -
320B PHE* 3.7 19.2 - + - -
323B GLU 3.6 20.9 - - - -
324B ASN 3.4 19.1 - - - -
325B TYR* 4.2 0.4 - - - -
326B VAL* 3.3 38.8 - - + +
331B ARG* 5.7 0.4 - - - -
334B LEU* 4.9 1.3 - - + -
345B ILE* 3.1 25.0 + - + -
346B LYS* 3.8 8.3 - - - +
348B TRP* 1.3 97.9 - + - +
350B GLN* 1.3 61.3 + - - +
352B ARG* 4.3 2.0 - - - -
353B ARG* 3.1 42.4 + - - +
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LYS* 3.1 14.0 + - - +
347B VAL* 3.1 26.2 + - - +
349B PHE* 1.3 79.8 - - - +
351B ASN* 1.3 79.4 + - - +
353B ARG* 3.5 17.5 + - - +
354B MET* 3.3 22.2 + - - +
204C T 3.0 25.7 + - - +
205C T 5.6 0.4 - - - -
215D C 4.6 25.4 - - + +
216D A 3.8 12.8 + - - +
217D A 3.3 17.0 + - - -
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Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B VAL* 2.9 25.9 + - - +
348B TRP* 3.7 6.6 - - + +
350B GLN* 1.3 90.2 + - - +
352B ARG* 1.3 59.4 + - - +
354B MET* 3.1 16.9 + - + +
355B LYS* 2.9 36.9 + - + +
201C T 6.0 1.1 - - + -
202C A 3.6 31.9 + - - +
203C A 2.9 46.9 + - - -
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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
----------------------------------------------------------
317B GLU* 3.0 39.7 + - - -
320B PHE* 3.5 37.6 - - + -
348B TRP* 2.8 50.0 + - + +
349B PHE 4.1 1.1 - - - +
351B ASN* 1.3 72.7 - - - +
353B ARG* 1.3 57.9 + - - +
355B LYS* 3.4 17.7 + - - +
356B ASP* 3.0 53.5 + - - +
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Residues in contact with ARG 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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320B PHE* 3.8 11.7 - - + -
324B ASN* 2.7 60.4 + - + +
325B TYR* 3.6 28.3 - - - +
346B LYS 5.4 0.8 + - - -
349B PHE* 3.1 33.6 + - - +
350B GLN* 3.8 20.8 - - - +
351B ASN 3.2 0.2 - - - -
352B ARG* 1.3 74.7 - - - +
354B MET* 1.3 57.3 + - - +
356B ASP* 3.5 2.7 - - + +
357B LYS* 2.8 36.8 + - - +
215D C 4.6 14.7 + - - -
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Residues in contact with MET 354 (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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350B GLN* 3.3 13.8 + - - +
351B ASN* 3.3 27.6 - - + +
353B ARG* 1.3 76.7 - - - +
355B LYS* 1.3 76.9 + - - +
357B LYS* 3.2 13.5 + - + +
358B ARG* 2.9 50.3 + - - +
359B GLN* 5.6 0.2 - - - +
201C T 6.4 0.9 - - + -
202C A 4.7 4.0 - - - +
203C A 3.5 16.2 - - - +
216D A 4.9 8.1 - - + +
217D A 3.3 33.2 - - - +
218D T 3.1 25.1 - - + +
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Residues in contact with LYS 355 (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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351B ASN* 2.9 24.5 + - + +
352B ARG* 3.4 29.2 - - - +
353B ARG 3.3 0.2 - - - -
354B MET* 1.3 89.7 - - + +
356B ASP* 1.3 57.1 + - - +
358B ARG 3.1 0.3 + - - -
359B GLN* 2.8 65.0 + - + +
201C T 3.8 59.5 - - + +
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Residues in contact with ASP 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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320B PHE* 3.6 27.0 - - + -
324B ASN* 4.8 6.6 - - - +
352B ARG* 3.0 29.1 + - - +
353B ARG* 3.5 5.8 - - - +
355B LYS* 1.3 76.5 - - - +
357B LYS* 1.3 61.5 + - - +
358B ARG 3.5 0.5 + - - -
359B GLN 4.3 8.2 + - - -
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Residues in contact with LYS 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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353B ARG 2.8 22.9 + - - +
354B MET* 3.5 13.1 - - + +
355B LYS 3.2 0.2 - - - -
356B ASP* 1.3 73.4 - - - +
358B ARG* 1.3 78.7 + - + +
216D A 3.5 55.5 + - - +
217D A 4.3 4.6 + - - -
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Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B MET* 2.9 30.7 + - - +
356B ASP 4.7 0.4 - - - -
357B LYS* 1.3 98.9 - - + +
359B GLN* 1.3 87.1 + - + +
216D A 4.5 1.2 - - - +
217D A 4.1 41.4 + - - +
218D T 3.6 30.9 + - - +
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Residues in contact with GLN 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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354B MET* 4.4 1.4 - - - +
355B LYS* 2.8 47.0 + - + +
356B ASP* 4.3 7.3 + - - -
358B ARG* 1.3 116.1 + - + +
201C T 5.8 2.4 - - - +
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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