Contacts of the helix formed by residues 332 - 352 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ARG* 6.1 1.3 - - - -
74A TYR* 5.2 11.0 - - - +
330A SER 4.5 2.2 - - - +
331A ASP* 1.3 76.0 - - - +
333A PHE* 1.3 68.4 + - - +
334A ASP* 3.3 17.2 + - - -
335A ILE* 3.0 28.1 + - - +
336A GLN* 3.0 17.7 + - - +
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Residues in contact with PHE 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ARG* 3.7 37.1 - - + +
70A PHE* 5.9 0.9 - + - -
74A TYR* 3.9 15.3 - + - -
96A VAL* 3.4 35.0 - - + -
99A HIS* 3.5 30.7 - - + +
100A LEU* 4.1 13.0 - - + +
105A PHE 3.6 17.9 - - - -
106A VAL* 3.4 33.2 - - + -
331A ASP 4.5 2.5 - - - -
332A THR* 1.3 78.1 - - - +
334A ASP* 1.3 57.8 + - - +
336A GLN* 3.2 21.3 + - - +
337A PHE* 3.0 23.2 + - - +
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Residues in contact with ASP 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 5.6 3.1 + - - +
99A HIS* 3.6 30.1 + - + +
144A TYR* 3.9 6.3 + - - +
332A THR* 3.3 20.3 + - - -
333A PHE* 1.3 75.0 + - - +
335A ILE* 1.3 80.6 + - - +
337A PHE* 3.5 3.1 + - - +
338A THR* 3.4 24.6 + - - -
402A SO4 5.6 1.8 + - - -
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ASP* 3.8 26.9 - - + +
332A THR* 3.0 27.0 + - + +
334A ASP* 1.3 87.1 - - - +
336A GLN* 1.3 56.4 + - - +
338A THR* 3.3 7.0 + - + -
339A SER* 2.9 31.2 + - - -
67B MET* 6.5 0.2 - - + -
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A HIS 4.9 0.2 - - - -
100A LEU* 4.1 21.4 - - + +
103A GLY 5.2 0.5 - - - +
104A GLY* 4.6 10.6 - - - -
105A PHE 4.2 6.6 + - - +
329A ASP* 3.2 45.1 + - - +
331A ASP* 2.8 24.7 + - + +
332A THR 3.0 12.8 + - - +
333A PHE* 3.2 21.6 + - - +
335A ILE* 1.3 73.9 - - - +
337A PHE* 1.3 61.1 + - - +
339A SER* 3.9 5.3 - - - -
340A ARG* 2.9 33.8 + - - +
52B GLU* 5.2 0.2 - - - +
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Residues in contact with PHE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU 4.0 0.7 - - - -
99A HIS 3.1 26.4 + - - +
101A TYR* 3.5 34.2 - + - -
144A TYR* 3.3 62.4 - + - +
289A LYS* 4.0 21.1 - - + -
292A PHE* 4.1 7.4 - + - -
333A PHE 3.0 11.8 + - - +
334A ASP 3.6 4.7 - - - +
336A GLN* 1.3 75.8 - - - +
338A THR* 1.3 78.0 + - - +
340A ARG* 4.3 1.8 - - - +
341A ARG* 3.3 48.8 + - - +
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Residues in contact with THR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LYS* 6.2 0.2 - - - +
334A ASP 3.4 11.3 + - - -
335A ILE* 3.3 10.4 + - - +
336A GLN 3.2 0.2 - - - -
337A PHE* 1.3 91.0 - - - +
339A SER* 1.3 59.9 + - - +
341A ARG* 3.4 4.4 + - - +
342A PHE* 2.9 35.2 + - + +
77B LYS* 6.2 1.6 - - - +
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ASP* 6.2 0.2 - - - -
335A ILE* 2.9 22.1 + - - -
336A GLN* 3.9 7.2 - - - -
338A THR* 1.3 81.1 - - - +
340A ARG* 1.3 61.2 + - - +
342A PHE* 3.5 6.0 + - - +
343A TYR* 2.9 42.5 + - - -
52B GLU* 3.2 20.6 + - - +
67B MET* 5.3 6.4 - - - +
71B HIS* 6.2 1.2 - - - -
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Residues in contact with ARG 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASN* 4.0 32.7 + - + +
103A GLY 5.3 4.8 + - - +
111A TYR* 5.6 0.4 + - - -
271A TYR* 3.0 41.3 + - - -
279A LEU* 5.3 1.7 - - - +
318A TRP* 3.8 15.7 - - - -
322A ILE* 3.6 26.6 - - - +
336A GLN 2.9 17.3 + - - +
337A PHE* 4.5 2.7 - - - +
339A SER* 1.3 77.2 - - - +
341A ARG* 1.3 58.4 + - - +
343A TYR* 3.4 2.5 + - - -
344A ILE* 3.0 41.8 + - + +
52B GLU* 3.1 31.8 + - - +
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Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TYR* 3.1 33.5 + - + +
102A ASN* 4.0 10.3 - - - +
283A TRP* 3.7 27.5 - - + -
286A PHE* 2.8 29.5 + - - +
287A SER 3.8 3.4 + - - -
289A LYS* 3.3 37.6 - - - +
292A PHE* 4.4 7.7 - - - -
337A PHE* 3.3 47.9 + - - +
338A THR* 4.0 3.7 - - - +
339A SER 3.3 0.2 - - - -
340A ARG* 1.3 74.0 - - - +
342A PHE* 1.3 66.6 + - - +
344A ILE* 3.6 7.2 - - + +
345A GLU* 2.8 27.0 + - - +
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Residues in contact with PHE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A THR* 2.9 21.9 + - + +
339A SER* 3.5 8.1 - - - +
341A ARG* 1.3 76.4 - - - +
343A TYR* 1.3 91.4 + + - +
345A GLU* 3.6 13.2 - - - +
346A LYS* 2.9 47.2 + - + +
75B GLU* 3.8 34.3 - - + -
77B LYS* 3.4 29.4 - - - -
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Residues in contact with TYR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A TYR* 3.8 23.8 - + + -
322A ILE* 3.7 24.0 - - + -
339A SER* 2.9 40.8 + - - -
340A ARG 3.9 2.0 - - - +
341A ARG 3.2 0.2 - - - -
342A PHE* 1.3 98.8 - + - +
344A ILE* 1.3 67.6 + - - +
346A LYS* 3.7 9.1 - - + +
347A ILE* 2.8 33.0 + - + +
50B ARG 3.9 4.2 + - - -
51B TYR* 3.1 41.7 - + + +
52B GLU* 3.5 25.5 + - + -
67B MET* 4.2 6.1 - - + +
71B HIS* 4.9 1.9 + - - -
75B GLU* 4.2 8.3 + - - -
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASN* 3.6 27.8 - - - +
279A LEU* 3.9 29.8 - - + +
280A ILE* 4.0 28.5 - - + +
283A TRP* 3.7 32.1 - - + -
318A TRP* 4.3 4.0 - - + -
322A ILE* 5.1 0.2 - - - +
340A ARG* 3.0 38.3 + - + +
341A ARG* 3.6 8.3 - - + +
343A TYR* 1.3 77.4 - - - +
345A GLU* 1.3 64.1 + - - +
347A ILE* 3.8 1.9 - - - +
348A TYR* 2.9 22.7 + - - +
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A TRP* 3.3 47.8 - - + +
341A ARG 2.8 17.3 + - - +
342A PHE* 3.6 13.5 - - - +
344A ILE* 1.3 74.4 - - - +
346A LYS* 1.3 63.0 + - - +
348A TYR* 3.2 1.4 + - - +
349A ASN* 2.9 45.3 + - - +
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Residues in contact with LYS 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A TYR* 3.5 40.2 - - + -
342A PHE* 2.9 47.0 + - + +
343A TYR* 3.7 13.7 - - + +
345A GLU* 1.3 73.6 - - - +
347A ILE* 1.3 65.9 + - + +
349A ASN* 3.3 5.3 + - - +
350A GLU* 3.0 35.2 + - + +
51B TYR* 5.8 1.6 - - - -
74B TYR* 6.6 0.2 - - - -
75B GLU* 6.3 0.8 - - - +
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Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE* 3.9 25.1 - - + -
314A ILE* 4.4 11.4 - - + +
317A LEU* 3.9 24.2 - - + +
318A TRP* 3.7 47.6 - - + +
321A TYR* 3.7 22.9 - - + -
322A ILE* 4.8 5.2 - - + -
343A TYR 2.8 26.8 + - - +
344A ILE 3.8 2.9 - - - +
346A LYS* 1.3 69.3 - - - +
348A TYR* 1.3 67.3 + - - +
350A GLU* 3.1 16.7 + - - +
351A LEU* 3.3 11.4 + - - +
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Residues in contact with TYR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE* 3.4 33.7 - - + +
281A MET* 4.1 12.6 - - + -
283A TRP* 3.9 20.9 - + + -
284A PRO* 3.4 33.9 - - + +
302A LEU* 5.3 2.3 - - - +
305A LYS* 5.4 3.3 + - - +
344A ILE 2.9 17.6 + - - +
345A GLU 3.6 3.4 - - - +
347A ILE* 1.3 75.8 - - - +
349A ASN* 1.3 76.6 + - - +
351A LEU* 3.0 30.9 + - + +
352A ASN 3.9 2.1 + - - -
353A ILE* 4.1 43.0 + - + +
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Residues in contact with ASN 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A TRP* 5.0 2.1 + - - +
345A GLU* 2.9 43.0 + - - +
346A LYS* 4.0 4.9 - - - +
348A TYR* 1.3 96.9 - - - +
350A GLU* 1.3 59.7 + - - +
351A LEU 3.2 0.4 + - - -
352A ASN* 3.6 18.0 + - - +
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A LYS* 5.2 9.9 + - - -
317A LEU* 3.6 25.9 - - + +
320A LYS* 5.0 1.7 + - - -
321A TYR* 2.4 41.9 + - - -
346A LYS* 3.0 26.2 + - + +
347A ILE 3.1 10.9 + - - +
349A ASN* 1.3 76.1 - - - +
351A LEU* 1.3 65.2 + - - +
352A ASN* 3.2 15.5 + - - -
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE* 4.0 11.0 - - + -
281A MET* 3.8 18.2 - - - -
310A LEU* 4.5 19.9 - - + +
313A LYS* 3.9 28.7 - - + -
314A ILE* 3.6 40.6 - - + -
317A LEU* 4.3 6.1 - - + -
347A ILE 3.4 14.4 - - - +
348A TYR* 3.0 13.5 + - + +
350A GLU* 1.3 77.1 - - - +
352A ASN* 1.3 70.6 + - - +
353A ILE* 3.9 17.3 - - + +
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Residues in contact with ASN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A TYR 3.9 2.2 + - - -
349A ASN* 3.6 16.2 + - - +
350A GLU* 3.2 18.1 + - - +
351A LEU* 1.3 82.4 + - - +
353A ILE* 1.3 64.4 + - - +
252E TYR* 5.4 9.2 + - + -
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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