Contacts of the helix formed by residues 332 - 351 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LYS* 5.1 16.6 - - - +
50E ARG* 5.9 1.6 - - - -
74E TYR* 5.7 6.3 - - - +
330E SER 3.6 1.9 + - - +
331E ASP* 1.3 77.1 + - - +
333E PHE* 1.3 61.9 + - - +
334E ASP* 3.1 20.0 + - - -
335E ILE* 3.1 23.8 + - - +
336E GLN* 2.9 24.8 + - - +
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Residues in contact with PHE 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ARG* 3.6 41.2 - - + +
70E PHE* 5.8 0.7 - + - -
74E TYR* 4.1 9.6 - + - -
96E VAL* 3.6 33.0 - - + -
99E HIS* 3.5 32.1 - - + +
100E LEU* 3.9 18.1 - - + +
105E PHE 3.4 20.0 - - - -
106E VAL* 3.5 34.1 - - + -
331E ASP 4.5 2.0 - - - -
332E THR* 1.3 77.6 - - - +
334E ASP* 1.3 57.8 + - - +
336E GLN* 3.4 16.1 + - - +
337E PHE 3.0 23.6 + - - -
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Residues in contact with ASP 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ARG* 5.3 4.5 + - - -
99E HIS* 3.8 28.0 + - + -
144E TYR* 4.1 7.1 + - - +
332E THR* 3.1 22.9 + - - -
333E PHE* 1.3 78.6 + - - +
335E ILE* 1.3 83.5 + - - +
337E PHE* 3.6 3.8 - - - +
338E THR* 3.4 22.9 + - - -
402E SO4 5.4 2.6 + - - -
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Residues in contact with ILE 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E ASP* 3.8 28.5 - - + +
332E THR* 3.1 24.0 + - + +
334E ASP* 1.3 90.3 + - - +
336E GLN* 1.3 61.1 + - - +
338E THR* 3.2 7.6 + - - +
339E SER* 2.9 31.8 + - - -
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Residues in contact with GLN 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E LEU* 4.1 22.9 - - + +
103E GLY 5.4 0.3 - - - +
104E GLY* 4.7 7.8 - - - -
105E PHE 4.3 7.1 + - - +
329E ASP* 3.3 45.6 + - - +
331E ASP* 2.6 26.5 + - + +
332E THR 2.9 15.5 + - - +
333E PHE* 3.4 20.1 + - - +
335E ILE* 1.3 74.8 - - - +
337E PHE* 1.3 66.8 + - - +
339E SER* 3.9 5.5 - - - -
340E ARG* 3.0 27.5 + - - +
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Residues in contact with PHE 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E LEU 4.4 0.4 - - - -
99E HIS* 3.3 28.9 + - - +
101E TYR* 3.5 31.4 - + - -
102E ASN* 5.7 0.2 + - - -
144E TYR* 3.4 63.5 - + - +
289E LYS* 4.0 19.1 - - + -
292E PHE* 4.1 7.6 - + - -
333E PHE 3.0 14.1 + - - +
334E ASP 3.6 4.9 - - - +
335E ILE 3.3 0.4 - - - -
336E GLN* 1.3 76.5 - - - +
338E THR* 1.3 76.2 + - - +
340E ARG* 4.2 2.6 - - - +
341E ARG* 3.3 51.4 + - - +
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Residues in contact with THR 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E LYS* 6.1 0.9 - - - +
334E ASP 3.4 11.7 + - - -
335E ILE* 3.2 12.0 + - - +
336E GLN 3.1 0.6 - - - -
337E PHE* 1.3 90.9 - - - +
339E SER* 1.3 61.0 + - - +
341E ARG* 3.7 4.9 - - - +
342E PHE* 2.9 31.1 + - + +
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Residues in contact with SER 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E ASP* 6.1 0.7 - - - -
335E ILE* 2.9 21.6 + - - -
336E GLN* 3.9 6.1 - - - -
338E THR* 1.3 79.9 - - - +
340E ARG* 1.3 63.5 + - - +
342E PHE* 3.1 7.0 + - - +
343E TYR* 3.1 46.1 + - - -
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Residues in contact with ARG 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ASN* 4.1 38.3 + - + +
103E GLY 5.1 4.2 + - - +
111E TYR* 5.5 0.6 + - - -
271E TYR* 3.0 40.1 + - - -
279E LEU* 5.7 1.1 - - + +
318E TRP* 3.9 15.0 - - + -
322E ILE* 3.8 39.9 - - - +
336E GLN 3.0 16.7 + - - +
337E PHE* 4.3 2.5 - - - +
339E SER* 1.3 77.3 + - - +
341E ARG* 1.3 57.4 + - - +
343E TYR* 3.3 3.7 + - - +
344E ILE* 3.0 38.5 + - + +
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Residues in contact with ARG 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E TYR* 3.0 32.2 + - + +
102E ASN* 4.1 8.7 - - - +
283E TRP* 3.4 31.1 - - + -
286E PHE* 2.7 32.3 + - - +
287E SER 3.5 4.6 + - - -
289E LYS* 3.4 34.3 - - - +
292E PHE* 4.4 8.9 - - - -
337E PHE* 3.3 49.9 + - - +
338E THR* 3.8 4.7 - - - +
339E SER 3.3 0.6 - - - -
340E ARG* 1.3 73.5 - - - +
342E PHE* 1.3 60.6 + - - +
344E ILE* 3.7 8.8 - - + +
345E GLU* 3.0 30.7 + - - +
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Residues in contact with PHE 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E THR* 2.9 23.4 + - + +
339E SER* 3.1 8.0 + - - +
341E ARG* 1.3 76.7 - - - +
343E TYR* 1.3 93.6 + + - +
345E GLU* 3.8 13.9 - - - +
346E LYS* 2.9 46.6 + - + +
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Residues in contact with TYR 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321E TYR* 3.8 40.6 - + + -
322E ILE* 3.8 31.0 - - + -
339E SER* 3.1 42.8 + - - +
340E ARG* 3.3 3.3 + - - +
342E PHE* 1.3 102.9 - + - +
344E ILE* 1.3 68.0 + - - +
346E LYS* 3.7 11.4 - - + +
347E ILE* 2.9 32.9 + - + +
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Residues in contact with ILE 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E TYR* 5.4 0.4 - - - +
102E ASN* 3.5 33.2 - - - +
279E LEU* 4.0 30.3 - - + +
280E ILE* 3.8 27.0 - - + +
283E TRP* 3.7 30.7 - - + -
318E TRP* 4.6 6.7 - - + -
340E ARG* 3.0 30.3 + - + +
341E ARG* 3.7 9.0 - - + +
342E PHE 3.3 0.2 - - - -
343E TYR* 1.3 77.7 - - - +
345E GLU* 1.3 62.1 + - - +
348E TYR* 3.1 21.5 + - - +
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Residues in contact with GLU 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E TRP* 3.4 45.9 + - + +
341E ARG 3.0 17.7 + - - +
342E PHE* 3.8 13.4 - - + +
344E ILE* 1.3 73.3 - - - +
346E LYS* 1.3 67.4 + - - +
348E TYR* 3.3 1.7 + - - +
349E ASN* 2.9 43.9 + - - +
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Residues in contact with LYS 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E TYR* 2.9 50.2 + - + -
342E PHE* 2.9 36.5 + - + +
343E TYR* 3.3 18.1 + - + +
345E GLU* 1.3 80.1 - - - +
347E ILE* 1.3 63.0 + - - +
349E ASN* 3.5 5.9 + - - +
350E GLU* 3.0 28.4 + - - +
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Residues in contact with ILE 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E ILE* 4.0 31.0 - - + -
314E ILE* 4.2 14.6 - - + +
317E LEU* 3.8 24.9 - - + +
318E TRP* 3.7 41.5 - - + +
321E TYR* 3.8 19.7 - - + -
322E ILE* 4.7 4.3 - - + -
343E TYR 2.9 19.5 + - - +
344E ILE 4.0 2.7 - - - +
346E LYS* 1.3 71.3 - - - +
348E TYR* 1.3 70.5 + - - +
350E GLU* 2.9 21.1 + - - +
351E LEU* 3.4 7.8 + - + +
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Residues in contact with TYR 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E ILE* 3.4 35.3 - - + +
281E MET* 4.2 17.3 - - + -
283E TRP* 3.7 19.7 - + + -
284E PRO* 3.4 33.6 - - + +
344E ILE 3.1 16.2 + - - +
345E GLU 3.6 3.1 - - - +
347E ILE* 1.3 78.0 - - - +
349E ASN* 1.3 82.2 + - - +
351E LEU* 2.8 30.9 + - + +
352E ASN 3.9 1.4 + - - -
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Residues in contact with ASN 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E TRP* 4.8 2.6 + - - +
345E GLU* 2.9 47.7 + - - +
346E LYS* 3.9 4.8 - - - +
348E TYR* 1.3 90.5 - - - +
350E GLU* 1.3 56.9 + - - +
351E LEU 3.0 0.2 - - - -
352E ASN* 3.1 28.6 + - - +
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Residues in contact with GLU 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E LYS* 4.6 14.2 - - - -
317E LEU* 3.6 31.1 - - + +
320E LYS* 4.5 5.5 + - - -
321E TYR* 2.8 33.0 + - - -
346E LYS* 3.0 20.8 + - - +
347E ILE 2.9 12.1 + - - +
349E ASN* 1.3 76.0 - - - +
351E LEU* 1.3 61.9 + - - +
352E ASN* 3.3 11.2 + - - -
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Residues in contact with LEU 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E ILE* 4.1 9.9 - - + -
281E MET* 3.9 22.4 - - - -
310E LEU* 4.2 27.0 - - + +
313E LYS* 3.7 32.1 - - + +
314E ILE* 3.8 33.9 - - + +
317E LEU* 4.6 4.3 - - + -
347E ILE 3.5 8.7 - - - +
348E TYR* 2.8 21.1 + - + +
350E GLU* 1.3 78.4 - - - +
352E ASN* 1.3 73.1 + - - +
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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