Contacts of the helix formed by residues 330 - 347 (chain A) in PDB entry 3LEE
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A PHE* 3.7 10.0 - - - -
327A ASP 4.9 0.4 + - - -
328A ALA 3.7 0.8 - - - -
329A THR* 1.3 89.3 + - - +
331A MET* 1.3 68.5 + - - +
332A PRO* 3.2 8.6 - - + +
333A ALA* 2.8 41.2 + - - +
334A VAL 2.9 9.9 + - - -
283C GLN* 3.8 21.1 + - + +
287C ASN* 3.5 10.0 + - - -
329C THR* 3.8 24.7 + - - +
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Residues in contact with MET 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 4.3 7.0 - - - +
277A LEU* 2.9 50.7 - - + +
278A SER* 3.5 25.6 - - - +
286A PHE* 3.1 33.7 - - + -
330A ASN* 1.3 70.9 - - - +
332A PRO* 1.3 58.4 - - + +
334A VAL* 3.0 18.5 + - - +
335A LYS* 2.5 57.3 + - + +
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Residues in contact with PRO 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASN* 3.2 13.5 - - + +
331A MET* 1.3 93.0 - - + +
333A ALA* 1.3 60.0 + - - +
335A LYS* 3.7 11.0 - - + -
336A ALA* 3.1 26.9 + - - +
60C ALA* 3.4 16.1 - - + +
62C ASP* 5.2 4.3 - - - +
283C GLN* 4.2 9.9 - - + -
284C SER* 3.9 37.0 - - - +
287C ASN* 3.7 15.3 + - + +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ASP* 2.8 34.8 - - - +
330A ASN* 2.8 31.1 + - - +
332A PRO* 1.3 73.4 - - - +
334A VAL* 1.3 65.8 + - - +
335A LYS 3.1 0.3 + - - -
336A ALA* 3.2 6.7 + - - +
337A ILE* 2.8 29.2 + - + +
287C ASN* 3.4 10.4 - - - +
329C THR* 4.8 2.5 - - + -
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 6.1 0.7 - - + -
277A LEU* 4.3 16.2 - - + -
286A PHE* 3.8 17.0 - - + -
290A ALA* 3.9 8.1 - - + -
294A VAL* 4.4 13.0 - - + -
327A ASP 4.3 0.6 + - - -
328A ALA* 3.7 29.6 - - + +
330A ASN 2.9 16.6 + - - +
331A MET* 3.1 23.8 - - - +
333A ALA* 1.3 72.3 - - - +
335A LYS* 1.3 59.4 + - + +
337A ILE* 3.2 10.4 + - - +
338A ILE* 2.8 39.5 + - + +
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Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 4.0 24.0 - - + -
278A SER* 4.3 7.1 + - - -
331A MET* 2.5 40.6 + - + +
332A PRO* 3.8 9.9 - - + +
334A VAL* 1.3 71.4 - - + +
336A ALA* 1.3 67.6 + - - +
338A ILE* 2.9 9.0 + - - +
339A TYR* 2.7 54.7 + - + +
370A ASN* 3.7 32.7 + - - -
59C GLN 4.9 3.4 - - - -
60C ALA* 4.0 18.2 + - + +
61C LEU 5.3 3.2 + - - -
62C ASP* 5.0 7.9 + - - +
191D GLU* 5.9 0.2 + - - -
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Residues in contact with ALA 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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332A PRO 3.1 16.2 + - - +
333A ALA* 3.4 6.5 - - - +
335A LYS* 1.3 77.6 - - - +
337A ILE* 1.3 57.3 + - + +
339A TYR* 3.2 1.0 + - - -
340A GLN* 2.9 34.2 + - - +
56C ALA* 3.6 34.0 - - + +
57C VAL* 4.6 12.3 - - + +
60C ALA* 4.0 3.8 - - + +
287C ASN* 5.9 0.7 - - - +
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A VAL* 3.8 23.3 - - + -
327A ASP* 3.6 48.0 - - + +
328A ALA* 4.0 13.7 - - + +
333A ALA* 2.8 19.7 + - - +
334A VAL* 3.5 6.3 - - - +
336A ALA* 1.3 72.8 - - + +
338A ILE* 1.3 66.0 + - + +
340A GLN* 3.3 14.4 + - - +
341A TYR* 3.0 51.2 + - + -
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Residues in contact with ILE 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 3.9 21.5 - - + +
273A VAL* 5.1 9.9 - - + -
274A ILE* 4.0 26.9 - - + -
277A LEU* 5.6 1.3 - - + -
293A GLN* 5.9 1.8 - - + -
294A VAL* 4.9 10.1 - - + +
297A ILE* 3.9 30.3 - - + -
334A VAL* 2.8 31.6 + - + +
335A LYS* 3.4 7.6 - - - +
337A ILE* 1.3 76.1 - - - +
339A TYR* 1.3 72.1 + - + +
340A GLN 3.0 1.2 + - - -
341A TYR* 3.1 9.8 + - - +
342A MET* 3.1 30.6 + - + +
366A ILE* 4.8 0.7 - - + -
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Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 4.0 15.5 - - + +
335A LYS* 2.7 56.4 + - + +
336A ALA 3.7 4.0 - - - +
338A ILE* 1.3 73.1 - - + +
340A GLN* 1.3 62.5 + - - +
342A MET* 3.3 8.7 - - + +
343A GLU* 3.3 19.4 + - - +
366A ILE* 3.3 38.8 + - + -
367A ARG* 4.7 4.9 - - + -
369A GLN 3.9 16.8 + - - -
370A ASN 4.3 0.3 + - - -
48C ASN* 5.2 3.8 - - - +
56C ALA* 3.7 17.9 - - + -
59C GLN* 3.2 61.6 + - + +
66C ARG* 4.1 2.7 + - - -
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Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA* 2.9 17.5 + - - +
337A ILE* 3.4 19.2 - - - +
339A TYR* 1.3 74.6 - - - +
341A TYR* 1.3 68.7 + - + +
343A GLU* 3.1 19.3 + - + +
344A GLU* 3.4 10.7 + - - +
53C SER* 5.1 12.9 - - - -
56C ALA* 4.4 13.1 - - + +
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Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A VAL* 4.7 6.9 - - + +
297A ILE* 3.8 26.5 - - + -
298A ALA* 3.9 27.8 - - + +
301A ALA* 3.9 23.3 - - + +
316A ILE* 5.0 5.4 - - + +
337A ILE* 3.0 44.6 + - + -
338A ILE* 3.1 6.1 + - - +
340A GLN* 1.3 82.5 - - + +
342A MET* 1.3 65.2 + - + +
344A GLU* 3.1 29.8 + - - +
345A ILE* 3.2 15.9 + - - +
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Residues in contact with MET 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.7 27.8 - - + -
270A ILE* 4.0 10.5 - - + -
297A ILE* 4.0 21.1 - - + +
338A ILE* 3.1 22.1 + - + +
339A TYR* 3.3 12.8 - - + +
340A GLN 3.1 0.2 - - - -
341A TYR* 1.3 78.5 - - + +
343A GLU* 1.3 57.3 + - - +
345A ILE* 3.2 11.2 - - + +
346A TYR* 2.9 23.0 + - - +
363A ILE* 3.1 37.1 - - + +
366A ILE* 3.7 43.3 - - + -
367A ARG* 5.9 4.0 - - + +
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Residues in contact with GLU 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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339A TYR 3.3 7.4 + - - +
340A GLN* 3.1 12.8 + - + +
342A MET* 1.3 77.9 - - - +
344A GLU* 1.3 58.3 + - - +
346A TYR* 3.0 13.0 + - - +
347A HIS* 2.7 41.2 + - + +
367A ARG* 2.7 31.0 + - - +
48C ASN* 3.2 39.0 - - - +
49C GLN* 5.3 0.2 - - - -
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Residues in contact with GLU 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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301A ALA* 4.9 11.4 - - + +
340A GLN 3.4 6.0 + - - +
341A TYR* 3.1 29.3 + - - +
343A GLU* 1.3 73.2 - - - +
345A ILE* 1.3 69.0 + - - +
347A HIS* 3.2 8.1 + - - -
348A ARG* 3.0 45.6 + - - +
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Residues in contact with ILE 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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263A ILE* 4.6 7.9 - - + -
267A LEU* 3.4 37.9 - - + -
297A ILE 6.0 0.2 - - - +
300A LEU* 5.0 2.7 - - + +
301A ALA* 4.4 21.5 - - + +
304A TYR* 3.9 24.1 - - + -
341A TYR 3.2 8.4 + - - +
342A MET* 3.2 20.2 - - + +
344A GLU* 1.3 80.8 - - - +
346A TYR* 1.3 65.4 + - - +
348A ARG* 3.0 13.8 + - - +
349A ILE* 3.3 10.5 + - + +
359A THR* 3.5 24.5 - - + -
363A ILE* 3.3 15.7 - - + -
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Residues in contact with TYR 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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342A MET 2.9 13.1 + - - +
343A GLU* 3.0 22.9 + - - +
345A ILE* 1.3 77.1 - - - +
347A HIS* 1.3 62.4 + - - +
348A ARG 3.0 5.4 + - - -
349A ILE* 3.3 28.5 + - + +
360A ARG* 4.0 41.3 - - + +
363A ILE* 3.9 16.8 - - + -
364A SER* 5.8 0.8 - - - -
367A ARG* 3.3 36.2 + - - +
45C LYS* 3.6 27.7 - - + +
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Residues in contact with HIS 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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343A GLU* 2.7 31.3 + - + +
344A GLU* 3.2 6.0 + - - +
345A ILE 3.2 0.2 + - - -
346A TYR* 1.3 75.7 - - + +
348A ARG* 1.3 62.6 + - + +
349A ILE 3.7 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