Contacts of the helix formed by residues 327 - 343 (chain B) in PDB entry 4L0D
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 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B PRO* 6.2 1.1 - - - -
283B GLU* 4.1 25.6 - - + +
301B TYR* 6.5 0.2 - - - -
303B VAL* 4.6 2.1 - - - +
326B SER* 1.3 80.7 + - - +
328B ASP* 1.3 64.1 + - - +
329B GLU* 3.2 31.9 - - - +
330B GLU* 2.9 33.8 + - - +
331B ALA* 3.3 21.7 + - - +
352B SER* 4.5 0.3 + - - -
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Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PRO* 6.0 0.2 - - - +
301B TYR* 3.5 15.4 - - - +
302B GLU* 2.8 36.2 + - - +
303B VAL* 2.9 34.2 + - - +
327B ASN* 1.3 76.1 - - - +
329B GLU* 1.3 66.9 + - - +
331B ALA* 3.0 3.6 + - - +
332B PHE* 2.9 32.0 + - + -
396B PHE* 3.6 23.0 - - + -
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Residues in contact with GLU 329 (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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327B ASN* 3.2 13.6 - - - +
328B ASP* 1.3 78.0 - - - +
330B GLU* 1.3 63.1 + - - +
332B PHE* 4.3 1.0 - - - +
333B THR* 2.7 42.7 + - - +
395B GLY 3.8 6.6 - - - +
396B PHE* 3.8 48.9 - - + +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LYS 4.2 4.1 - - - +
326B SER* 3.4 15.0 - - - -
327B ASN* 2.9 40.1 + - - +
329B GLU* 1.3 79.5 - - - +
331B ALA* 1.3 65.3 + - - +
333B THR* 3.6 2.4 - - - -
334B PHE* 2.9 40.7 + - + +
355B ALA* 4.1 26.3 - - + +
356B VAL* 5.7 1.0 - - - +
359B LYS* 5.5 8.0 + - - +
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 3.8 14.1 - - + -
327B ASN 3.3 10.4 + - - +
328B ASP 3.0 9.3 + - - +
330B GLU* 1.3 81.0 - - - +
332B PHE* 1.3 62.0 + - + +
335B ALA* 2.9 24.6 + - - +
348B GLY 3.7 9.0 - - - +
351B GLY* 3.3 11.2 - - - -
352B SER* 3.2 36.3 - - - +
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Residues in contact with PHE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLU* 3.9 22.0 - - + -
303B VAL* 4.1 22.9 - - + -
328B ASP* 2.9 23.3 + - + +
329B GLU* 4.3 2.0 - - - +
331B ALA* 1.3 74.7 - - - +
333B THR* 1.3 66.8 + - - +
335B ALA* 3.6 2.8 - - - +
336B ARG* 2.9 31.8 + - - +
348B GLY* 4.3 15.7 - - - -
381B TYR* 6.4 1.1 - + - -
385B PHE* 3.6 33.0 - + + -
390B TRP* 3.8 16.8 - + - -
391B MET* 3.8 20.4 - - + -
396B PHE* 3.6 37.5 - + - -
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLU* 2.7 36.5 + - - +
330B GLU* 3.6 5.2 - - - -
332B PHE* 1.3 76.9 - - - +
334B PHE* 1.3 65.3 + - + +
336B ARG* 3.6 6.8 + - - +
337B MET* 2.9 47.3 + - + +
391B MET* 5.0 4.5 - - - +
396B PHE 5.0 4.3 + - - -
397B LEU* 5.8 2.3 - - - +
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Residues in contact with PHE 334 (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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95B ILE* 4.4 3.6 - - + -
99B PHE* 3.3 46.9 - + - -
330B GLU* 2.9 34.6 + - + +
333B THR* 1.3 85.2 - - + +
335B ALA* 1.3 61.4 + - - +
337B MET* 3.7 12.3 - - + +
338B LEU* 2.9 32.4 + - - +
351B GLY* 3.5 19.3 - - - +
354B VAL* 3.7 21.0 - - + +
355B ALA* 3.7 16.6 - - + -
358B VAL* 3.9 28.9 - - + -
359B LYS* 5.8 1.8 - - - -
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Residues in contact with ALA 335 (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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331B ALA 2.9 17.7 + - - +
332B PHE* 3.2 6.0 + - - +
334B PHE* 1.3 74.4 - - - +
336B ARG* 1.3 60.2 + - - +
338B LEU* 3.0 8.1 + - - +
339B ILE* 2.9 32.4 + - - +
346B CYS* 4.6 3.2 - - - +
347B GLY 4.0 15.5 - - - +
348B GLY* 4.1 2.9 - - - -
351B GLY* 3.9 7.4 - - - +
385B PHE* 3.5 30.5 - - + -
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Residues in contact with ARG 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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183A ALA* 4.8 2.1 - - + +
332B PHE 2.9 19.8 + - - +
333B THR* 3.9 5.6 - - - +
335B ALA* 1.3 72.7 - - - +
337B MET* 1.3 61.3 + - - +
339B ILE* 3.4 9.4 + - + +
340B ALA* 2.9 32.4 + - - +
385B PHE* 3.1 33.9 + - + +
386B LEU* 3.9 11.6 + - - +
388B ASP* 2.9 46.5 + - - +
391B MET* 3.9 21.8 - - - +
397B LEU* 4.3 17.0 - - - +
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Residues in contact with MET 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.6 16.3 - - + +
98B LYS* 4.1 17.9 - - - +
99B PHE* 3.8 36.6 - - + -
333B THR* 2.9 38.1 + - + +
334B PHE* 3.8 14.1 - - + +
336B ARG* 1.3 76.9 - - - +
338B LEU* 1.3 57.5 + - - +
340B ALA* 4.7 2.9 - - - -
341B GLN* 2.9 50.8 + - + +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 4.8 7.0 - - + -
95B ILE* 3.7 21.5 - - + -
334B PHE 2.9 19.3 + - - +
335B ALA 3.0 7.4 + - - +
337B MET* 1.3 74.7 - - - +
339B ILE* 1.3 60.7 + - - +
342B GLU* 2.9 43.2 + - + +
343B GLY 3.4 1.6 + - - -
344B LEU* 3.5 21.3 + - + -
346B CYS* 3.5 26.5 - - - -
350B ALA* 4.5 7.6 - - + +
351B GLY 5.0 0.7 - - - +
354B VAL* 4.2 31.0 - - + -
374B LEU* 4.3 14.1 - - + -
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Residues in contact with ILE 339 (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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183A ALA* 4.1 27.1 - - + +
184A LEU* 4.0 14.9 - - + +
335B ALA 2.9 19.6 + - - +
336B ARG* 3.8 8.1 - - + +
338B LEU* 1.3 75.3 - - - +
340B ALA* 1.3 59.0 + - - +
343B GLY* 2.8 29.1 + - - -
344B LEU 3.1 20.4 - - - +
345B LEU* 3.6 26.9 - - + -
346B CYS* 4.3 6.1 - - - +
378B VAL* 3.6 28.5 - - + -
385B PHE* 4.4 12.1 - - + -
386B LEU* 5.0 5.6 - - + -
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Residues in contact with ALA 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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159A ALA* 3.2 29.5 - - - +
183A ALA 3.5 20.6 - - - +
184A LEU* 4.3 9.8 - - - +
185A GLY* 5.8 1.6 - - - -
336B ARG 2.9 17.5 + - - +
337B MET* 4.2 3.1 - - - +
339B ILE* 1.3 77.3 - - - +
341B GLN* 1.3 61.6 + - + +
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Residues in contact with GLN 341 (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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159A ALA 3.7 10.4 - - - +
160A VAL* 4.4 2.9 - - - +
94B LYS* 3.1 52.5 + - + +
95B ILE* 4.1 15.9 - - + -
98B LYS* 4.4 23.6 - - - +
337B MET* 2.9 39.2 + - + +
340B ALA* 1.3 78.8 - - + +
342B GLU* 1.3 62.0 + - - +
343B GLY 3.5 0.4 + - - -
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Residues in contact with GLU 342 (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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79A ASP* 5.9 1.2 - - - +
80A ILE* 3.5 17.0 + - - +
160A VAL* 4.1 7.7 - - - +
91B ARG 4.2 3.8 - - - +
92B ILE* 3.1 27.0 - - + +
93B ASN* 2.9 27.7 + - - +
94B LYS* 2.6 32.5 + - - -
95B ILE* 3.4 12.7 + - + -
338B LEU* 2.9 25.0 + - + +
341B GLN* 1.3 80.8 - - - +
343B GLY* 1.3 64.0 + - - +
344B LEU* 3.2 20.2 + - + +
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Residues in contact with GLY 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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80A ILE* 3.8 14.4 - - - +
114A ALA* 5.7 0.3 - - - +
156A LEU* 3.4 35.8 - - - +
159A ALA* 5.1 2.4 - - - +
160A VAL* 4.7 3.5 - - - +
184A LEU* 4.6 2.9 - - - -
339B ILE* 2.8 18.5 + - - -
340B ALA 4.4 0.6 + - - -
341B GLN 3.5 1.6 - - - -
342B GLU* 1.3 79.3 - - - +
344B LEU* 1.3 61.5 + - - +
345B LEU* 3.6 8.8 + - - +
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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