Contacts of the helix formed by residues 332 - 351 (chain B) in PDB entry 4PEI
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 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A LYS* 5.4 11.2 - - - +
50B ARG* 6.2 0.7 - - - -
74B TYR* 5.9 5.2 - - - +
330B SER 3.7 1.7 + - - +
331B ASP* 1.3 76.4 + - - +
333B PHE* 1.3 59.8 + - - +
334B ASP* 3.2 17.2 + - - -
335B ILE* 2.9 31.6 + - - +
336B GLN* 2.9 23.4 + - - +
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Residues in contact with PHE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 3.6 43.7 - - + +
70B PHE* 5.9 0.7 - + - -
74B TYR* 4.1 10.3 - + - -
96B VAL* 3.8 29.4 - - + -
99B HIS* 3.6 28.2 - - + +
100B LEU* 3.9 15.2 - - + +
105B PHE 3.5 20.2 - - - -
106B VAL* 3.4 33.0 - - + -
331B ASP 4.4 2.2 - - - -
332B THR* 1.3 71.2 - - - +
334B ASP* 1.3 61.9 + - - +
336B GLN* 3.2 22.2 + - - +
337B PHE* 2.9 27.9 + - - +
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Residues in contact with ASP 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 5.4 4.2 + - - -
99B HIS* 3.7 29.3 + - + +
144B TYR* 3.9 6.9 + - - +
332B THR* 3.2 25.0 + - - +
333B PHE* 1.3 75.0 + - - +
335B ILE* 1.3 70.8 + - - +
337B PHE* 3.4 4.2 - - - +
338B THR* 3.4 22.9 + - - -
402B SO4 5.6 2.3 + - - -
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Residues in contact with ILE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ASP* 3.9 27.1 - - + +
332B THR* 2.9 29.4 + - - +
334B ASP* 1.3 83.0 - - - +
336B GLN* 1.3 69.5 + - - +
338B THR* 3.1 7.6 + - - +
339B SER* 2.9 27.1 + - - -
67E MET* 6.3 1.1 - - + -
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.0 16.7 - - + +
103B GLY 5.1 0.5 - - - +
104B GLY* 4.6 8.3 - - - -
105B PHE 4.3 7.2 + - - +
329B ASP* 3.3 48.3 + - - +
331B ASP* 2.8 26.0 + - + +
332B THR 2.9 14.4 + - - +
333B PHE* 3.6 29.0 - - - +
335B ILE* 1.3 78.7 - - - +
337B PHE* 1.3 61.5 + - - +
339B SER* 3.9 5.9 - - - -
340B ARG* 3.0 27.7 + - - +
52E GLU* 5.2 0.2 - - - +
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Residues in contact with PHE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU 4.2 0.4 - - - -
99B HIS 3.4 26.6 + - - +
101B TYR* 3.4 32.3 - + - -
102B ASN* 5.7 0.3 + - - -
144B TYR* 3.5 60.8 - + - +
289B LYS* 4.0 21.3 - - + -
292B PHE* 4.1 7.4 - + - -
333B PHE 2.9 10.4 + - - +
334B ASP 3.4 9.2 - - - +
336B GLN* 1.3 77.5 - - - +
338B THR* 1.3 74.9 + - - +
340B ARG* 3.5 2.7 + - - +
341B ARG* 3.2 48.1 + - - +
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Residues in contact with THR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LYS* 5.9 2.6 + - - +
334B ASP 3.4 11.5 + - - -
335B ILE* 3.1 10.8 + - - -
337B PHE* 1.3 86.6 - - - +
339B SER* 1.3 62.0 + - - +
341B ARG* 3.5 4.4 + - - +
342B PHE* 2.9 30.5 + - + +
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ASP* 6.0 1.6 - - - -
335B ILE* 2.9 21.5 + - - -
336B GLN* 3.9 6.5 - - - -
338B THR* 1.3 78.4 - - - +
340B ARG* 1.3 63.3 + - - +
342B PHE* 3.0 14.4 + - - +
343B TYR* 3.0 35.1 + - - -
52E GLU* 2.8 28.1 + - - +
67E MET* 5.4 6.1 - - - +
71E HIS* 6.2 3.1 - - - -
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Residues in contact with ARG 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASN* 4.1 30.5 + - + +
103B GLY 5.5 3.7 + - - +
111B TYR* 5.6 0.2 + - - -
271B TYR* 3.0 43.9 + - - -
279B LEU* 5.3 0.8 - - + +
318B TRP* 3.9 22.2 - - - -
322B ILE* 3.8 19.1 - - - +
336B GLN 3.0 17.4 + - - +
337B PHE* 4.2 2.2 - - - +
339B SER* 1.3 76.8 - - - +
341B ARG* 1.3 58.5 + - - +
343B TYR* 3.3 2.6 + - - -
344B ILE* 3.0 46.5 + - + +
52E GLU* 2.7 33.4 + - - +
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Residues in contact with ARG 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR* 2.8 34.0 + - + +
102B ASN* 4.1 8.3 - - - +
283B TRP* 3.7 23.0 - - + -
286B PHE* 2.9 30.7 + - - +
287B SER 3.5 9.3 + - - -
289B LYS* 3.4 35.0 - - - +
292B PHE* 4.6 7.5 - - - -
337B PHE* 3.2 51.6 + - - +
338B THR* 4.0 4.5 - - - +
340B ARG* 1.3 73.9 - - - +
342B PHE* 1.3 64.9 + - - +
344B ILE* 3.9 7.0 - - + +
345B GLU* 3.0 25.5 + - - +
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Residues in contact with PHE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B THR* 2.9 19.2 + - + +
339B SER* 3.0 11.8 + - - +
341B ARG* 1.3 76.0 - - - +
343B TYR* 1.3 90.2 + + - +
345B GLU* 3.7 11.4 - - - +
346B LYS* 2.9 51.3 + - + +
71E HIS* 5.9 1.1 - + - -
75E GLU* 3.6 38.1 - - + -
77E LYS* 3.7 27.8 - - - -
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Residues in contact with TYR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B TYR* 3.6 29.2 - + + -
322B ILE* 3.8 24.2 - - + -
339B SER* 3.0 37.4 + - - -
340B ARG* 4.0 2.9 - - - +
342B PHE* 1.3 98.5 - + - +
344B ILE* 1.3 63.8 + - - +
346B LYS* 4.2 7.9 - - + -
347B ILE* 2.9 34.3 + - + +
50E ARG 3.8 1.9 + - - -
51E TYR* 3.2 38.9 - + + +
52E GLU* 3.7 26.6 + - + -
67E MET* 4.6 4.9 - - + +
71E HIS* 4.6 2.5 + + - -
75E GLU* 3.8 15.1 + - - -
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR* 5.5 0.2 - - - +
102B ASN* 3.6 27.1 - - - +
279B LEU* 3.8 51.6 - - + +
280B ILE* 3.9 23.1 - - + +
283B TRP* 3.9 21.8 - - + -
318B TRP* 4.4 7.6 - - + -
340B ARG* 3.0 30.2 + - + +
341B ARG* 3.9 7.2 - - + +
342B PHE 3.3 0.2 - - - -
343B TYR* 1.3 77.8 - - - +
345B GLU* 1.3 63.3 + - - +
347B ILE* 3.4 2.1 + - - +
348B TYR* 3.0 22.5 + - - +
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Residues in contact with GLU 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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283B TRP* 3.4 48.7 + - + +
341B ARG 3.0 15.1 + - - +
342B PHE* 3.7 11.6 - - - +
344B ILE* 1.3 78.3 - - - +
346B LYS* 1.3 57.5 + - - +
348B TYR* 3.5 1.9 + - - +
349B ASN* 2.9 46.7 + - - +
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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
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321B TYR* 3.4 41.5 - - + -
342B PHE* 2.9 39.4 + - + +
343B TYR* 3.7 17.9 - - + +
344B ILE 3.3 0.2 - - - -
345B GLU* 1.3 75.6 - - - +
347B ILE* 1.3 61.8 + - + +
349B ASN* 3.4 6.8 + - - +
350B GLU* 3.0 39.9 + - + +
75E GLU* 5.9 3.4 - - - +
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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
----------------------------------------------------------
280B ILE* 3.9 22.0 - - + -
314B ILE* 4.2 16.4 - - + +
317B LEU* 3.7 24.7 - - + +
318B TRP* 3.7 48.2 - - + +
321B TYR* 3.8 21.5 - - + -
322B ILE* 4.4 7.0 - - + -
343B TYR* 2.9 19.2 + - + +
344B ILE 3.9 2.7 - - - +
346B LYS* 1.3 75.4 - - - +
348B TYR* 1.3 62.2 + - - +
350B GLU* 3.0 16.7 + - - +
351B LEU* 3.3 13.8 + - + +
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Residues in contact with TYR 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 3.1 34.0 - - + +
281B MET* 4.2 10.1 - - + -
283B TRP* 3.7 28.9 - + + -
284B PRO* 3.5 31.9 - - + +
302B LEU* 5.4 2.2 - - + +
305B LYS* 5.5 4.0 + - - -
344B ILE 3.0 18.4 + - - +
345B GLU 3.7 3.4 - - - +
347B ILE* 1.3 75.3 - - - +
349B ASN* 1.3 75.2 - - - +
351B LEU* 3.2 21.2 + - + +
352B ASN 3.9 2.1 + - - -
353B ILE* 3.7 44.6 + - + +
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Residues in contact with ASN 349 (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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283B TRP* 5.2 1.9 + - - -
345B GLU* 2.9 43.5 + - - +
346B LYS* 3.7 7.2 - - - +
347B ILE 3.3 0.2 - - - -
348B TYR* 1.3 89.7 - - - +
350B GLU* 1.3 63.4 + - + +
352B ASN* 3.2 21.7 + - - +
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LYS* 3.4 18.0 + - - +
317B LEU* 3.7 33.6 - - + +
320B LYS* 5.3 1.4 + - - -
321B TYR* 2.6 31.4 + - - -
346B LYS* 3.0 31.1 + - + +
347B ILE 3.0 6.1 + - - +
349B ASN* 1.3 77.8 - - + +
351B LEU* 1.3 60.3 + - - +
352B ASN* 3.2 16.9 + - - -
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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
----------------------------------------------------------
280B ILE* 3.8 16.2 - - + -
281B MET* 3.9 14.6 - - - -
310B LEU* 4.1 24.2 - - + +
313B LYS* 3.9 34.7 - - + +
314B ILE* 3.7 43.3 - - + +
317B LEU* 4.7 2.5 - - + -
347B ILE 3.3 11.9 - - - +
348B TYR* 3.2 12.2 + - + +
350B GLU* 1.3 75.0 - - - +
352B ASN* 1.3 75.0 + - - +
353B ILE* 3.7 16.0 - - + +
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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