Contacts of the helix formed by residues 330 - 349 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A GLN* 3.9 20.2 - - + +
287A ASN* 3.6 5.7 + - - -
329A THR* 3.5 32.9 + - - +
286B PHE* 3.6 6.2 - - - -
329B THR* 1.3 87.8 + - - +
331B MET* 1.3 63.7 + - - +
332B PRO* 3.5 10.2 - - + +
333B ALA* 2.9 35.8 + - - +
334B VAL* 3.0 21.3 + - - +
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Residues in contact with MET 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 3.8 33.9 - - + +
277B LEU* 3.7 21.5 - - + +
278B SER* 4.0 17.5 - - - -
286B PHE* 3.4 32.4 - - + -
330B ASN* 1.3 68.8 - - - +
332B PRO* 1.3 69.8 - - + +
334B VAL* 3.1 12.9 + - + +
335B LYS* 2.8 64.0 + - + +
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Residues in contact with PRO 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 3.4 21.8 - - + +
62A ASP* 4.8 7.2 - - - +
283A GLN* 4.0 12.1 - - + -
284A SER* 3.7 45.1 - - - +
287A ASN* 3.8 14.1 - - + +
330B ASN* 3.5 8.5 - - + +
331B MET* 1.3 93.3 - - + +
333B ALA* 1.3 60.2 + - - +
335B LYS* 3.3 3.9 + - + -
336B ALA* 3.0 20.4 + - - +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASN* 3.8 10.9 - - - +
329A THR* 4.5 6.7 - - + -
328B ALA* 5.4 1.3 - - - +
329B THR 5.3 3.4 - - - +
330B ASN* 2.9 34.7 + - - +
332B PRO* 1.3 77.1 - - - +
334B VAL* 1.3 57.8 - - + +
336B ALA* 3.5 6.0 + - - +
337B ILE* 2.9 43.1 + - + +
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.8 21.8 - - + -
286B PHE* 3.5 23.8 - - + -
290B ALA* 4.2 3.1 - - + -
294B VAL* 4.1 11.2 - - + -
328B ALA* 3.8 24.2 - - + +
330B ASN 3.0 18.9 + - - +
331B MET* 3.5 14.6 - - + +
333B ALA* 1.3 72.9 - - - +
335B LYS* 1.3 67.2 + - - +
337B ILE* 3.3 7.7 + - - +
338B ILE* 2.9 49.3 + - + +
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Residues in contact with LYS 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 3.8 26.7 + - + +
61A LEU 4.9 4.6 + - - -
62A ASP* 4.8 11.3 + - - +
274B ILE* 4.2 15.0 - - + -
278B SER* 5.3 5.8 - - - -
331B MET* 2.8 39.8 + - + +
332B PRO* 3.5 11.4 - - + +
333B ALA 3.3 0.2 - - - -
334B VAL* 1.3 78.1 - - - +
336B ALA* 1.3 57.0 + - - +
338B ILE* 3.4 5.5 + - - +
339B TYR* 2.9 49.8 + - + +
370B ASN* 3.4 45.8 + - - +
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 3.4 38.1 - - + +
57A VAL* 4.2 15.3 - - + +
60A ALA* 4.1 1.5 - - + +
332B PRO 3.0 16.5 + - - +
333B ALA* 3.8 6.7 - - - +
335B LYS* 1.3 77.9 - - - +
337B ILE* 1.3 57.8 + - + +
339B TYR* 3.3 0.7 + - - -
340B GLN* 2.9 28.1 + - - +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B VAL* 3.6 28.7 - - + -
328B ALA* 4.3 27.8 - - + +
333B ALA* 2.9 28.7 + - + +
334B VAL* 3.7 5.6 - - - +
336B ALA* 1.3 75.5 - - + +
338B ILE* 1.3 64.1 + - - +
340B GLN* 3.3 7.4 + - - +
341B TYR* 3.2 36.0 + - + -
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Residues in contact with ILE 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ILE* 3.9 20.4 - - + -
273B VAL* 5.0 4.5 - - + -
274B ILE* 4.3 25.4 - - + -
277B LEU* 4.8 7.6 - - + -
293B GLN* 5.8 0.7 - - + -
294B VAL* 4.5 10.3 - - + -
297B ILE* 3.4 43.7 - - + -
334B VAL* 2.9 40.3 + - + +
335B LYS* 3.7 4.7 - - - +
337B ILE* 1.3 75.4 - - + +
339B TYR* 1.3 69.3 + - + +
341B TYR* 3.1 6.7 + - - +
342B MET* 2.9 25.8 + - - +
366B ILE* 5.1 0.2 - - + -
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Residues in contact with TYR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 3.4 31.0 - - + -
59A GLN* 3.5 41.5 - - + +
66A ARG* 3.7 6.9 + - - -
274B ILE* 4.1 11.9 - - + +
335B LYS* 2.9 38.6 + - + +
336B ALA 3.5 4.5 - - - +
338B ILE* 1.3 76.4 - - + +
340B GLN* 1.3 62.8 + - - +
342B MET* 3.0 18.2 + - + +
343B GLU* 3.0 21.1 + - + +
366B ILE* 3.7 40.6 + - + -
367B ARG* 5.2 0.9 - - + -
369B GLN* 5.4 0.2 - - - +
370B ASN* 2.9 35.0 + - - -
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Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG 3.7 7.5 + - - +
53A SER* 3.3 44.1 + - - +
56A ALA* 4.1 5.9 - - + +
336B ALA 2.9 17.1 + - - +
337B ILE* 3.7 7.0 - - - +
338B ILE 3.2 0.2 - - - -
339B TYR* 1.3 76.3 - - - +
341B TYR* 1.3 63.8 + - + +
343B GLU* 3.0 27.6 + - - +
344B GLU* 3.0 19.3 + - - +
347B HIS* 5.6 1.6 - - - -
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Residues in contact with TYR 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B VAL* 4.5 7.2 - - + -
297B ILE* 3.7 21.1 - - + -
298B ALA* 3.5 40.0 - - + +
301B ALA* 3.7 19.0 - - + +
337B ILE* 3.2 40.4 + - + -
338B ILE* 3.1 7.6 + - - +
340B GLN* 1.3 78.5 - - + +
342B MET* 1.3 63.6 + - - +
344B GLU* 3.0 43.7 - - - +
345B ILE* 3.2 13.6 + - - +
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Residues in contact with MET 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 3.4 45.3 - - + -
270B ILE* 4.6 12.6 - - - -
297B ILE* 5.0 7.4 - - + -
338B ILE* 2.9 21.6 + - - +
339B TYR* 3.0 17.2 + - + +
341B TYR* 1.3 78.9 - - - +
343B GLU* 1.3 59.1 + - - +
345B ILE* 3.4 15.2 + - + +
346B TYR* 3.0 21.5 + - - +
363B ILE* 3.4 39.7 - - + +
366B ILE* 4.3 29.2 - - + -
367B ARG* 6.2 0.7 - - + -
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Residues in contact with GLU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN* 3.2 30.2 - - + +
52A ARG 5.8 1.8 - - - +
56A ALA* 6.2 2.0 - - + -
59A GLN* 4.9 1.4 + - - +
339B TYR* 3.0 15.5 + - + +
340B GLN* 3.0 23.6 + - - +
342B MET* 1.3 74.9 - - - +
344B GLU* 1.3 59.4 + - - +
346B TYR* 3.1 8.6 + - - +
347B HIS* 2.9 52.0 + - + -
363B ILE* 4.5 3.0 - - - +
367B ARG* 2.9 50.9 + - - +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ALA* 4.3 16.1 - - + +
302B ALA* 5.4 1.0 + - - -
340B GLN* 3.0 14.4 + - - +
341B TYR* 3.0 47.8 + - - +
343B GLU* 1.3 79.6 - - - +
345B ILE* 1.3 60.3 + - - +
347B HIS* 3.4 7.5 + - - +
348B ARG* 3.4 30.6 + - + +
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Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ILE* 4.4 7.9 - - + -
267B LEU* 4.0 17.3 - - + -
297B ILE* 5.4 2.0 - - + +
300B LEU* 4.4 5.6 - - + -
301B ALA* 3.7 35.4 - - + +
304B TYR* 3.6 36.7 - - + -
341B TYR 3.2 5.9 + - - +
342B MET* 3.8 27.8 - - + +
344B GLU* 1.3 78.3 - - - +
346B TYR* 1.3 65.9 + - - +
348B ARG* 2.9 15.8 + - - +
349B ILE* 3.2 10.4 + - - +
359B THR* 4.0 9.0 - - + -
363B ILE* 4.0 13.5 - - + -
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Residues in contact with TYR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 4.7 13.8 - - + +
49A GLN* 5.9 0.6 + - + -
342B MET 3.0 14.4 + - - +
343B GLU* 3.2 17.3 - - - +
345B ILE* 1.3 78.6 - - - +
347B HIS* 1.3 76.3 + + - +
349B ILE* 3.2 35.3 + - + +
360B ARG* 4.0 37.7 + - + +
363B ILE* 3.8 15.2 - - + +
364B SER* 4.9 0.7 + - - -
367B ARG* 3.1 39.2 + - - +
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Residues in contact with HIS 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN 5.7 3.0 + - - -
52A ARG* 5.5 7.0 - - - -
340B GLN* 5.6 1.8 - - - -
343B GLU* 2.9 40.6 + - + +
344B GLU* 3.4 7.3 + - - +
345B ILE 3.3 0.2 - - - -
346B TYR* 1.3 89.7 - + - +
348B ARG* 1.3 59.2 + - - +
349B ILE 3.4 1.8 + - - +
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Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ALA 2.7 28.9 + - - -
302B ALA* 3.0 22.2 + - - +
304B TYR* 2.5 51.0 + - + -
305B ASN* 4.0 15.2 + - + +
306B ASN* 4.4 9.3 - - - +
344B GLU* 3.4 19.8 + - + +
345B ILE* 2.9 11.5 + - - +
347B HIS* 1.3 77.1 - - + +
349B ILE* 1.3 65.7 + - - +
350B PRO* 3.1 11.6 - - - +
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B TYR* 3.3 16.8 - - + +
345B ILE 3.2 10.3 + - - +
346B TYR* 3.2 38.4 + - + +
347B HIS 3.4 2.3 - - - +
348B ARG* 1.3 75.1 - - - +
350B PRO* 1.3 66.0 - - - +
351B ASP* 3.7 4.2 + - - +
356B SER* 3.6 35.0 - - - +
359B THR* 3.8 18.8 - - + -
360B ARG* 3.7 43.2 + - + +
363B ILE* 4.3 0.9 - - + -
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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