Contacts of the helix formed by residues 332 - 351 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D ARG* 5.7 2.5 - - - -
74D TYR* 5.3 9.6 - - - +
330D SER 3.7 2.0 + - - +
331D ASP* 1.3 77.9 + - - +
333D PHE* 1.3 67.8 + - - +
334D ASP* 3.2 17.2 + - - -
335D ILE* 3.1 27.0 + - - +
336D GLN* 3.0 17.8 + - - +
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Residues in contact with PHE 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ARG* 3.6 37.8 - - + +
70D PHE* 5.8 0.4 - + - -
74D TYR* 4.0 14.1 - + - -
96D VAL* 3.5 35.0 - - + -
99D HIS* 3.5 32.4 - - + +
100D LEU* 4.0 14.6 - - + -
105D PHE 3.7 17.9 - - - -
106D VAL* 3.4 30.5 - - + -
330D SER* 6.5 0.2 - - - -
331D ASP 4.4 3.4 - - - -
332D THR* 1.3 78.6 - - - +
334D ASP* 1.3 58.2 + - - +
336D GLN* 3.5 18.6 - - - +
337D PHE 2.9 23.6 + - - -
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Residues in contact with ASP 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ARG* 5.1 4.9 + - - -
99D HIS* 3.7 28.8 + - + +
144D TYR* 3.9 7.2 + - - +
332D THR* 3.2 21.2 + - - -
333D PHE* 1.3 75.8 + - - +
335D ILE* 1.3 78.8 + - - +
337D PHE* 3.5 3.6 - - - +
338D THR* 3.3 24.9 + - - -
402D SO4 5.7 1.1 + - - -
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Residues in contact with ILE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ASP* 4.0 27.4 - - + +
332D THR* 3.1 27.0 + - - +
334D ASP* 1.3 84.9 - - - +
336D GLN* 1.3 65.4 + - - +
338D THR* 3.2 7.2 + - - -
339D SER* 2.9 27.0 + - - -
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Residues in contact with GLN 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D HIS 5.0 0.2 - - - -
100D LEU* 4.1 19.8 - - + +
103D GLY 5.1 0.7 - - - +
104D GLY* 4.5 10.7 - - - -
105D PHE 4.2 8.2 + - - -
329D ASP* 3.1 49.5 + - - +
330D SER* 4.6 0.2 - - - +
331D ASP* 2.9 25.5 + - + +
332D THR 3.0 16.0 + - - +
333D PHE* 3.5 20.8 - - - +
335D ILE* 1.3 77.6 - - - +
337D PHE* 1.3 62.3 - - - +
339D SER* 3.9 5.6 - - - -
340D ARG* 3.0 27.0 + - - +
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Residues in contact with PHE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU 4.2 0.2 - - - -
99D HIS 3.4 24.4 + - - +
101D TYR* 3.5 32.5 - + - -
144D TYR* 3.4 62.8 - + - +
289D LYS* 4.0 15.9 - - + -
292D PHE* 3.9 12.6 - + - -
333D PHE 2.9 11.5 + - - +
334D ASP 3.5 8.1 - - - +
336D GLN* 1.3 77.9 - - - +
338D THR* 1.3 75.7 + - - +
340D ARG* 4.3 1.7 - - - +
341D ARG* 3.2 51.9 + - - +
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Residues in contact with THR 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D LYS* 6.0 1.6 - - - +
334D ASP 3.3 12.3 + - - -
335D ILE* 3.2 10.2 + - - -
337D PHE* 1.3 90.8 - - - +
339D SER* 1.3 58.9 + - - +
341D ARG* 3.6 5.0 + - - +
342D PHE* 3.0 28.7 + - + +
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Residues in contact with SER 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D ILE* 2.9 22.1 + - - -
336D GLN* 3.9 7.2 - - - -
337D PHE 3.3 0.2 - - - -
338D THR* 1.3 76.1 - - - +
340D ARG* 1.3 66.0 + - - +
342D PHE* 3.1 14.1 + - - +
343D TYR* 3.1 37.2 + - - -
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Residues in contact with ARG 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASN* 4.0 32.5 + - + +
103D GLY 5.4 2.8 + - - -
111D TYR* 5.6 0.2 + - - -
271D TYR* 3.2 39.9 + - - -
279D LEU* 5.3 0.7 - - - -
318D TRP* 4.0 12.8 - - - -
322D ILE* 3.7 38.9 - - - +
329D ASP* 5.6 3.8 + - - -
336D GLN 3.0 17.1 + - - +
337D PHE* 4.3 2.2 - - - +
339D SER* 1.3 76.5 - - - +
341D ARG* 1.3 63.3 + - - +
342D PHE 3.3 0.2 + - - -
343D TYR* 3.4 2.8 + - - -
344D ILE* 3.1 42.1 + - + +
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Residues in contact with ARG 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR* 3.0 30.8 + - + +
102D ASN* 4.1 8.1 - - - +
283D TRP* 3.5 28.4 - - + -
286D PHE* 2.8 31.7 + - - +
287D SER 3.5 4.0 + - - -
289D LYS* 3.4 33.6 - - - +
292D PHE* 4.4 8.7 - - - -
337D PHE* 3.2 53.3 + - - +
338D THR* 4.0 4.0 - - - +
340D ARG* 1.3 78.8 - - - +
342D PHE* 1.3 63.5 + - - +
344D ILE* 3.7 9.1 - - + +
345D GLU* 3.0 27.1 + - - +
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Residues in contact with PHE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D THR* 3.0 21.7 + - + +
339D SER* 3.1 9.1 + - - +
341D ARG* 1.3 76.5 - - - +
343D TYR* 1.3 94.5 + + - +
345D GLU* 3.6 13.1 - - - +
346D LYS* 2.8 50.5 + - + +
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Residues in contact with TYR 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D TYR* 3.7 40.4 - + + -
322D ILE* 3.8 29.4 - - + -
339D SER* 3.1 40.9 + - - +
340D ARG* 3.4 2.4 + - - +
342D PHE* 1.3 102.6 - + + +
344D ILE* 1.3 61.0 + - - +
346D LYS* 3.7 10.7 - - + +
347D ILE* 2.9 37.9 + - + +
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Residues in contact with ILE 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASN* 3.6 27.1 - - - +
279D LEU* 3.7 36.1 - - + +
280D ILE* 3.5 24.0 - - + +
283D TRP* 3.7 30.3 - - + -
318D TRP* 4.5 5.8 - - + -
340D ARG* 3.1 32.0 + - + +
341D ARG* 3.7 7.2 - - + +
342D PHE 3.3 0.2 - - - -
343D TYR* 1.3 77.1 - - - +
345D GLU* 1.3 59.4 + - - +
347D ILE* 3.4 0.4 + - - -
348D TYR* 2.8 28.4 + - - +
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Residues in contact with GLU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D TRP* 3.6 46.2 + - + +
341D ARG 3.0 17.3 + - - +
342D PHE* 3.6 12.7 - - - +
344D ILE* 1.3 75.0 - - - +
346D LYS* 1.3 66.3 + - - +
348D TYR* 3.3 0.7 + - - +
349D ASN* 2.9 43.6 + - - +
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Residues in contact with LYS 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D TYR* 3.5 39.7 - - + -
342D PHE* 2.8 47.0 + - + +
343D TYR* 3.7 15.0 - - + +
344D ILE 3.3 0.2 - - - -
345D GLU* 1.3 74.7 - - - +
347D ILE* 1.3 61.9 - - - +
349D ASN* 3.3 6.6 + - - +
350D GLU* 3.1 36.5 + - + +
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Residues in contact with ILE 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ILE* 3.7 26.7 - - + -
314D ILE* 4.5 15.3 - - + +
317D LEU* 4.1 26.9 - - + +
318D TRP* 3.7 44.4 - - + -
321D TYR* 3.8 22.0 - - + -
322D ILE* 4.5 5.8 - - + -
343D TYR* 2.9 25.7 + - + +
346D LYS* 1.3 72.0 - - - +
348D TYR* 1.3 68.0 + - - +
350D GLU* 3.2 12.3 + - - +
351D LEU* 3.4 13.1 + - + +
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Residues in contact with TYR 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ILE* 3.3 33.6 - - + +
281D MET* 4.3 9.2 - - - -
283D TRP* 3.7 25.8 - + + -
284D PRO* 3.5 32.0 - - + +
302D LEU* 5.5 1.3 - - + +
305D LYS* 5.1 6.1 + - - +
344D ILE 2.8 21.3 + - - +
345D GLU 3.7 3.1 - - - +
347D ILE* 1.3 73.9 - - - +
349D ASN* 1.3 76.2 + - - +
351D LEU* 3.1 22.0 + - + +
352D ASN 4.0 1.7 + - - -
353D ILE* 3.8 46.8 + - + +
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Residues in contact with ASN 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D TRP* 5.0 2.1 + - - +
345D GLU* 2.9 44.1 + - - +
346D LYS* 3.8 5.5 - - - +
347D ILE 3.3 0.2 - - - -
348D TYR* 1.3 93.2 - - - +
350D GLU* 1.3 60.6 + - + +
352D ASN* 3.3 18.9 + - - +
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Residues in contact with GLU 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D LYS* 4.8 11.4 + - - -
317D LEU* 3.3 30.5 - - + +
321D TYR* 2.7 36.4 + - - -
346D LYS* 3.1 32.5 + - + +
347D ILE 3.2 6.0 + - - +
349D ASN* 1.3 73.4 - - + +
351D LEU* 1.3 61.7 + - - +
352D ASN* 2.8 23.0 + - - +
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Residues in contact with LEU 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ILE* 4.1 9.9 - - + -
281D MET* 3.8 24.5 - - - -
310D LEU* 4.2 23.0 - - + +
313D LYS* 3.6 31.4 - - + -
314D ILE* 3.8 33.7 - - + +
317D LEU* 4.8 3.4 - - + -
347D ILE* 3.4 14.5 + - + +
348D TYR* 3.1 10.2 + - + +
350D GLU* 1.3 73.2 - - - +
352D ASN* 1.3 79.8 + - - +
353D ILE* 3.9 16.7 - - + +
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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
------------------------------------------------------------
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