Contacts of the helix formed by residues 332 - 352 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C ARG* 5.8 2.5 - - - -
74C TYR* 5.3 9.9 - - - +
330C SER 3.8 1.8 + - - +
331C ASP* 1.3 77.2 + - - +
333C PHE* 1.3 63.9 + - - +
334C ASP* 3.0 19.8 + - - -
335C ILE* 3.0 23.5 + - - +
336C GLN* 2.9 23.2 + - - +
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Residues in contact with PHE 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ARG* 3.7 38.5 - - + +
70C PHE* 5.8 0.7 - + - -
74C TYR* 4.1 13.0 - + - -
96C VAL* 3.4 35.0 - - + -
99C HIS* 3.6 25.2 - - + +
100C LEU* 3.8 13.7 - - + -
105C PHE 3.6 18.6 - - - -
106C VAL* 3.5 31.4 - - + -
329C ASP 5.8 0.2 - - - -
331C ASP 4.5 3.1 - - - -
332C THR* 1.3 77.7 - - - +
334C ASP* 1.3 57.7 + - - +
336C GLN* 3.1 22.2 + - - +
337C PHE* 2.8 29.6 + - - +
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Residues in contact with ASP 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ARG* 5.4 4.2 + - - +
99C HIS* 3.8 29.1 - - + +
144C TYR* 3.9 6.8 + - - +
332C THR* 3.0 22.3 + - - -
333C PHE* 1.3 78.6 + - - +
335C ILE* 1.3 68.7 + - - +
337C PHE* 3.3 14.0 - - - +
338C THR* 3.4 13.2 + - - -
402C SO4 5.6 2.1 + - - +
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Residues in contact with ILE 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ASP* 4.1 26.0 - - + +
332C THR* 3.0 26.6 + - - +
334C ASP* 1.3 83.7 - - - +
336C GLN* 1.3 67.6 + - - +
337C PHE 3.1 0.2 - - - -
338C THR* 3.1 6.9 + - - +
339C SER* 2.9 27.2 + - - -
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Residues in contact with GLN 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C HIS 4.9 0.2 - - - -
100C LEU* 4.1 19.5 - - + +
103C GLY 5.1 0.5 - - - +
104C GLY* 4.4 13.3 - - - -
105C PHE 4.1 8.3 + - - -
329C ASP* 3.2 45.3 + - - +
331C ASP* 2.9 26.7 + - + +
332C THR 2.9 12.8 + - - +
333C PHE* 3.1 22.2 + - - +
335C ILE* 1.3 77.8 - - - +
337C PHE* 1.3 62.6 + - - +
339C SER* 3.9 5.1 - - - -
340C ARG* 3.0 27.9 + - - +
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Residues in contact with PHE 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C HIS* 3.3 25.7 + - - +
101C TYR* 3.5 31.5 - + - -
102C ASN* 5.6 0.2 + - - -
144C TYR* 3.4 60.8 - + - +
289C LYS* 4.1 18.4 - - + -
292C PHE* 4.2 6.7 - + - -
333C PHE 2.8 10.2 + - - +
334C ASP 3.3 9.4 - - - +
335C ILE 3.1 0.2 - - - -
336C GLN* 1.3 76.5 - - - +
338C THR* 1.3 76.3 + - - +
340C ARG* 4.2 2.7 - - - +
341C ARG* 3.2 52.0 + - - +
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Residues in contact with THR 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C ASP 3.4 11.7 + - - -
335C ILE* 3.1 9.7 + - - -
337C PHE* 1.3 89.4 - - - +
339C SER* 1.3 56.7 + - - +
341C ARG* 3.4 5.0 + - - +
342C PHE* 2.8 37.5 + - + +
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Residues in contact with SER 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C ASP* 5.7 0.8 + - - -
335C ILE* 2.9 21.3 + - - -
336C GLN* 3.9 6.5 - - - -
338C THR* 1.3 79.2 - - - +
340C ARG* 1.3 63.7 + - - +
342C PHE* 3.0 16.3 + - - +
343C TYR* 3.1 38.1 - - - -
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Residues in contact with ARG 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ASN* 3.9 38.0 + - + +
103C GLY 5.3 4.1 + - - +
111C TYR* 5.4 0.2 + - - -
271C TYR* 2.9 42.6 + - - -
279C LEU* 5.4 1.2 - - - +
318C TRP* 4.0 13.0 - - - -
322C ILE* 3.8 38.2 - - - +
336C GLN 3.0 18.4 + - - +
337C PHE* 4.2 2.9 - - - +
339C SER* 1.3 76.9 + - - +
341C ARG* 1.3 63.5 + - - +
343C TYR* 3.3 4.7 + - - -
344C ILE* 3.0 30.8 + - + +
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Residues in contact with ARG 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TYR* 3.0 32.4 + - + +
102C ASN* 4.1 8.5 - - - +
283C TRP* 3.5 28.6 - - + -
286C PHE* 2.8 31.9 + - - +
287C SER 3.7 4.2 + - - -
289C LYS* 3.3 33.2 - - - +
292C PHE* 4.2 10.7 - - - -
337C PHE* 3.2 51.7 + - - +
338C THR* 3.8 3.4 - - - +
340C ARG* 1.3 75.4 - - - +
342C PHE* 1.3 65.9 + - - +
344C ILE* 3.7 7.9 - - + +
345C GLU* 3.0 26.4 + - - +
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Residues in contact with PHE 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C THR* 2.8 23.0 + - + +
339C SER* 3.1 15.7 - - - +
341C ARG* 1.3 74.4 - - - +
343C TYR* 1.3 89.8 + + - +
345C GLU* 3.7 13.0 - - - +
346C LYS* 2.9 48.5 + - + +
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Residues in contact with TYR 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C TYR* 3.7 44.6 - + + -
322C ILE* 3.6 30.7 - - + -
339C SER* 3.1 41.9 + - - -
340C ARG* 4.0 4.7 - - - +
341C ARG 3.2 0.2 - - - -
342C PHE* 1.3 100.6 - + - +
344C ILE* 1.3 59.9 + - - +
345C GLU 3.3 0.2 - - - -
346C LYS* 4.0 8.1 - - + -
347C ILE* 2.8 39.5 + - + +
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Residues in contact with ILE 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TYR* 5.5 0.2 - - - +
102C ASN* 3.5 28.3 - - - +
279C LEU* 3.8 35.4 - - + +
280C ILE* 3.9 28.6 - - + +
283C TRP* 3.6 33.4 - - + -
318C TRP* 4.3 7.4 - - + -
340C ARG* 3.0 29.4 + - + +
341C ARG* 3.7 6.7 - - + +
343C TYR* 1.3 77.8 - - - +
345C GLU* 1.3 57.2 + - - +
347C ILE* 3.3 2.1 + - - +
348C TYR* 2.9 28.6 + - - +
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Residues in contact with GLU 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C TRP* 3.5 46.8 + - + +
341C ARG 3.0 18.4 + - - +
342C PHE* 3.7 12.9 - - - +
344C ILE* 1.3 77.8 - - - +
346C LYS* 1.3 63.7 + - - +
348C TYR* 3.3 1.2 + - - +
349C ASN* 2.9 43.8 + - - +
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Residues in contact with LYS 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C TYR* 3.6 38.3 + - + -
342C PHE* 2.9 46.2 + - + +
343C TYR* 3.7 14.1 - - + +
344C ILE 3.3 0.2 - - - -
345C GLU* 1.3 77.9 - - - +
347C ILE* 1.3 62.8 + - + +
349C ASN* 3.5 6.0 + - - +
350C GLU* 3.2 40.4 + - + +
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Residues in contact with ILE 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ILE* 4.0 22.4 - - + -
314C ILE* 4.3 13.7 - - - +
317C LEU* 3.8 22.7 - - + +
318C TRP* 3.6 49.1 - - + +
321C TYR* 3.9 20.6 - - + -
322C ILE* 4.6 5.2 - - + -
343C TYR 2.8 29.1 + - - +
344C ILE 3.8 3.1 - - - +
346C LYS* 1.3 72.0 - - - +
348C TYR* 1.3 65.3 + - - +
350C GLU* 3.1 17.1 + - - +
351C LEU* 3.3 13.5 + - + +
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Residues in contact with TYR 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ILE* 3.3 32.5 - - + +
281C MET* 4.2 12.3 - - + -
283C TRP* 3.8 26.7 - + + -
284C PRO* 3.4 33.7 - - + +
302C LEU* 5.4 2.1 - - + +
344C ILE 2.9 21.0 + - - +
345C GLU 3.7 3.4 - - - +
347C ILE* 1.3 72.9 - - - +
349C ASN* 1.3 74.8 + - - +
351C LEU* 3.1 22.4 + - + +
352C ASN 4.1 1.6 + - - -
353C ILE* 3.7 42.8 - - + +
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Residues in contact with ASN 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C TRP* 5.0 2.3 + - - -
345C GLU* 2.9 42.8 + - - +
346C LYS* 3.8 6.5 - - - +
348C TYR* 1.3 91.1 - - - +
350C GLU* 1.3 62.1 + - + +
351C LEU 3.1 1.7 + - - -
352C ASN* 3.5 12.5 + - - +
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Residues in contact with GLU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C LYS* 5.1 9.5 + - - -
317C LEU* 3.8 24.4 - - + +
320C LYS* 5.3 1.2 + - - -
321C TYR* 2.4 38.6 + - - -
346C LYS* 3.2 31.7 + - + +
347C ILE* 3.1 7.9 + - - +
349C ASN* 1.3 75.1 - - + +
351C LEU* 1.3 65.3 + - - +
352C ASN* 3.4 3.3 - - - +
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Residues in contact with LEU 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ILE* 4.1 11.2 - - + -
281C MET* 3.9 16.8 - - - -
310C LEU* 4.7 15.2 - - + +
313C LYS* 4.0 26.0 - - + -
314C ILE* 3.8 33.4 - - + -
317C LEU* 4.5 7.9 - - + -
347C ILE* 3.3 15.9 - - + +
348C TYR* 3.1 9.6 + - + +
350C GLU* 1.3 79.4 - - - +
352C ASN* 1.3 78.7 - - - +
353C ILE* 3.3 29.8 - - + +
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Residues in contact with ASN 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C TYR 4.1 1.4 + - - -
349C ASN 3.5 11.1 + - - +
350C GLU 3.4 5.3 - - - +
351C LEU* 1.3 87.0 - - - +
353C ILE* 1.3 67.7 + - - +
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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
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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