Contacts of the helix formed by residues 330 - 349 (chain C) in PDB entry 1EZF
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 ASN 330 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B GLN* 3.7 20.5 + - + +
287B ASN* 3.4 10.2 + - - -
329B THR* 3.6 27.1 + - - +
286C PHE* 3.6 7.1 - - - -
329C THR* 1.3 86.2 + - - +
331C MET* 1.3 65.0 + - - +
332C PRO* 3.4 8.8 - - + +
333C ALA* 3.0 42.7 + - - +
334C VAL* 3.0 19.8 + - - +
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Residues in contact with MET 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ILE* 3.7 30.7 - - + +
277C LEU* 3.7 35.4 - - + -
278C SER* 4.0 18.2 - - - +
286C PHE* 3.7 19.2 - - + -
330C ASN* 1.3 71.2 - - - +
332C PRO* 1.3 72.5 - - + +
334C VAL* 3.0 16.3 + - + +
335C LYS* 2.9 58.8 + - + +
338C ILE* 5.3 0.4 - - + -
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Residues in contact with PRO 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA* 3.3 25.0 - - + +
62B ASP* 4.6 6.7 - - - +
283B GLN* 3.9 12.1 - - + -
284B SER* 3.8 40.2 - - - +
287B ASN* 3.7 18.2 + - + +
330C ASN* 3.4 8.7 - - + +
331C MET* 1.3 93.6 - - + +
333C ALA* 1.3 59.7 + - - +
335C LYS* 3.7 4.2 + - + -
336C ALA* 3.2 19.6 + - - +
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Residues in contact with ALA 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASN* 4.0 9.0 - - - +
329B THR* 4.5 7.4 - - + -
328C ALA* 5.0 11.4 - - - +
330C ASN* 3.0 36.3 + - - +
332C PRO* 1.3 74.3 - - - +
334C VAL* 1.3 60.6 + - - +
336C ALA* 3.3 6.4 + - - +
337C ILE* 2.9 40.1 + - + +
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Residues in contact with VAL 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C LEU* 3.9 21.5 - - + -
286C PHE* 3.5 25.1 - - + -
290C ALA* 4.1 2.9 - - + -
294C VAL* 4.4 11.7 - - + -
328C ALA* 3.7 23.6 - - + +
330C ASN 3.0 18.3 + - - +
331C MET* 3.0 14.8 + - + +
333C ALA* 1.3 74.5 - - - +
335C LYS* 1.3 65.2 + - - +
337C ILE* 3.3 8.3 + - - +
338C ILE* 2.9 47.3 + - + +
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Residues in contact with LYS 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN 5.0 0.6 + - - -
60B ALA* 4.2 23.5 + - + +
61B LEU 5.2 4.2 + - - -
62B ASP* 5.2 6.3 + - - +
274C ILE* 4.1 16.4 - - + -
278C SER* 5.4 5.1 - - - -
331C MET* 2.9 42.5 + - + +
332C PRO* 3.8 6.5 - - + +
334C VAL* 1.3 74.8 - - - +
336C ALA* 1.3 54.0 + - - +
338C ILE* 3.1 10.9 + - - +
339C TYR* 2.7 56.2 + - + +
370C ASN* 3.2 37.9 + - - +
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Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 3.4 38.4 + - + +
57B VAL* 4.5 11.7 - - + +
60B ALA* 4.4 2.5 - - + -
332C PRO 3.2 15.4 + - - +
333C ALA* 3.5 7.2 - - - +
335C LYS* 1.3 79.0 - - - +
337C ILE* 1.3 60.7 + - + +
339C TYR* 3.3 0.6 + - - -
340C GLN* 2.9 28.6 + - - +
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Residues in contact with ILE 337 (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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294C VAL* 3.6 31.6 - - + -
297C ILE* 4.6 0.4 - - + -
328C ALA* 5.3 12.1 - - + +
333C ALA* 2.9 33.3 + - + +
334C VAL* 3.5 8.5 - - - +
336C ALA* 1.3 78.5 - - + +
338C ILE* 1.3 64.2 + - - +
340C GLN* 3.3 6.6 + - - +
341C TYR* 3.1 38.0 + - + -
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Residues in contact with ILE 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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270C ILE* 3.9 29.8 - - + -
273C VAL* 4.9 7.9 - - + -
274C ILE* 4.1 24.9 - - + -
277C LEU* 4.9 8.5 - - + -
293C GLN* 5.8 2.9 - - + -
294C VAL* 5.0 4.0 - - + -
297C ILE* 3.4 30.5 - - + -
331C MET* 5.3 0.9 - - + -
334C VAL* 2.9 39.5 + - + +
335C LYS* 3.5 7.9 - - - +
337C ILE* 1.3 75.3 - - - +
339C TYR* 1.3 66.1 + - + +
341C TYR* 3.0 6.1 + - - +
342C MET* 3.0 29.5 + - - +
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Residues in contact with TYR 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 3.5 27.8 - - + -
59B GLN* 3.3 45.8 - - + +
66B ARG* 3.2 7.9 + - - -
274C ILE* 3.9 13.7 - - + +
335C LYS* 2.7 40.1 + - + +
336C ALA 3.7 3.8 - - - +
338C ILE* 1.3 75.9 - - + +
340C GLN* 1.3 62.5 + - - +
342C MET* 3.2 9.0 + - + +
343C GLU* 3.1 27.3 + - + +
366C ILE* 3.4 38.3 + - + -
367C ARG* 5.1 0.9 - - + -
370C ASN* 2.7 36.4 + - - -
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Residues in contact with GLN 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG 3.9 9.3 + - - +
53B SER* 3.5 36.4 - - - +
56B ALA* 4.0 7.6 + - + +
336C ALA 2.9 17.6 + - - +
337C ILE* 3.7 7.2 - - - +
339C TYR* 1.3 76.7 - - - +
341C TYR* 1.3 63.9 + - + +
343C GLU* 3.2 17.2 + - - +
344C GLU* 3.2 22.0 + - - +
347C HIS* 5.8 1.8 - - - -
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Residues in contact with TYR 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C VAL* 4.4 5.4 - - + +
297C ILE* 3.5 32.5 - - + -
298C ALA* 3.7 31.5 - - + +
301C ALA* 3.8 18.8 - - + +
337C ILE* 3.1 39.6 + - + -
338C ILE 3.0 8.3 + - - +
340C GLN* 1.3 75.1 - - + +
342C MET* 1.3 68.4 + - + +
344C GLU* 3.1 42.4 + - - +
345C ILE* 3.2 7.1 + - - +
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Residues in contact with MET 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 3.4 33.2 - - + -
270C ILE* 4.5 12.6 - - + -
297C ILE* 5.3 6.5 - - + +
338C ILE* 3.0 28.7 + - + +
339C TYR* 3.2 14.1 + - + +
341C TYR* 1.3 82.3 - - + +
343C GLU* 1.3 65.8 + - - +
345C ILE* 3.1 19.6 + - + +
346C TYR* 2.9 26.3 + - - +
363C ILE* 3.8 28.1 - - + +
366C ILE* 4.4 26.0 - - + -
367C ARG* 6.0 0.9 - - + -
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Residues in contact with GLU 343 (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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48B ASN* 3.2 29.8 - - - +
52B ARG 5.5 2.7 - - - +
56B ALA* 6.1 2.0 - - + +
59B GLN* 5.2 1.4 + - - +
339C TYR* 3.1 16.0 + - + +
340C GLN* 3.2 23.7 + - - +
342C MET* 1.3 77.4 - - - +
344C GLU* 1.3 61.2 + - - +
346C TYR* 3.6 8.6 - - - +
347C HIS* 2.7 51.1 + - + -
363C ILE* 4.1 5.9 - - - +
367C ARG* 2.9 47.3 + - - +
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Residues in contact with GLU 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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301C ALA* 3.4 18.9 - - + +
302C ALA* 4.3 2.6 + - - +
340C GLN* 3.2 11.4 + - - +
341C TYR* 3.1 42.3 + - - +
343C GLU* 1.3 77.4 - - - +
345C ILE* 1.3 63.7 + - - +
347C HIS* 3.6 6.4 + - - +
348C ARG* 3.1 50.4 + - - +
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Residues in contact with ILE 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C ILE* 4.4 11.2 - - + -
267C LEU* 4.0 17.3 - - + -
297C ILE 5.4 0.4 - - - +
300C LEU* 4.4 2.5 - - + -
301C ALA* 3.7 33.7 - - + +
304C TYR* 3.7 33.3 - - + -
341C TYR 3.9 4.3 - - - +
342C MET* 3.1 32.2 + - + +
344C GLU* 1.3 75.3 - - - +
346C TYR* 1.3 67.0 + - - +
348C ARG* 2.9 15.6 + - - +
349C ILE* 3.2 10.2 + - - +
359C THR* 4.1 13.5 - - + -
363C ILE* 4.0 15.3 - - + -
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Residues in contact with TYR 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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45B LYS* 4.1 15.1 - - + +
342C MET 2.9 14.7 + - - +
343C GLU* 3.3 17.9 + - - +
345C ILE* 1.3 76.4 - - - +
347C HIS* 1.3 75.4 + + - +
348C ARG 3.2 0.7 + - - -
349C ILE* 3.2 30.9 + - + +
360C ARG* 3.7 37.4 - - + -
363C ILE* 3.9 22.6 - - + +
364C SER* 6.4 0.2 - - - -
367C ARG* 3.4 37.6 + - - -
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Residues in contact with HIS 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN 5.0 10.2 + - - -
52B ARG* 5.1 10.1 - - - -
340C GLN* 5.8 2.2 + - - -
343C GLU* 2.7 43.8 + - + +
344C GLU* 4.0 5.8 - - - +
346C TYR* 1.3 85.1 - + - +
348C ARG* 1.3 60.4 + - + +
349C ILE 3.7 3.2 + - - +
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Residues in contact with ARG 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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301C ALA 2.9 22.2 + - - -
302C ALA* 3.3 20.4 + - - +
304C TYR* 2.7 50.5 + - + -
305C ASN* 4.0 13.2 + - + +
306C ASN* 4.5 4.8 - - - +
344C GLU* 3.1 38.3 + - + +
345C ILE 2.9 10.1 + - - +
347C HIS* 1.3 78.9 - - + +
349C ILE* 1.3 64.3 + - - +
350C PRO* 3.0 12.1 - - - +
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Residues in contact with ILE 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C TYR* 3.4 16.4 - - - +
345C ILE 3.2 9.6 + - - +
346C TYR* 3.2 32.4 + - + +
347C HIS 3.4 3.0 - - - +
348C ARG* 1.3 74.8 - - - +
350C PRO* 1.3 67.4 - - + +
351C ASP* 4.0 2.1 + - - +
356C SER* 3.5 34.5 - - - +
359C THR* 3.8 23.6 - - + -
360C ARG* 3.5 38.1 - - + +
363C ILE* 4.5 0.4 - - + -
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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