Contacts of the helix formed by residues 336 - 354 (chain B) in PDB entry 4BL8
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 GLN 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 5.4 3.4 + - - +
170B PHE* 3.7 28.0 - - + -
179B ILE* 3.1 48.9 - - + +
334B ILE* 3.0 19.0 + - + +
335B PRO* 1.3 88.3 - - - +
337B MET* 1.3 63.7 + - - +
338B SER 3.4 0.4 - - - -
339B ALA* 3.4 14.5 - - + +
340B PHE 3.2 16.8 + - - -
369B ALA 5.3 4.0 - - - +
370B ALA 5.8 0.9 - - - +
372B PRO* 5.8 8.2 - - + +
375B HIS* 5.1 6.7 - - + -
531B PRO* 5.7 7.1 - - - +
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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
----------------------------------------------------------
66B ASP* 4.1 19.5 - - + +
169B ALA* 5.0 2.7 - - - -
170B PHE* 4.1 15.9 - - - -
259B PHE* 5.0 3.1 - - + -
331B MET* 4.9 3.1 - - + -
332B PRO* 3.3 53.4 - - + +
334B ILE* 3.1 19.6 + - + +
335B PRO 3.1 1.4 - - - -
336B GLN* 1.3 75.9 - - - +
338B SER* 1.3 66.0 + - - +
340B PHE* 3.1 20.4 + - + +
341B TRP* 2.9 71.9 + - + +
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Residues in contact with SER 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 3.6 41.3 - - - +
335B PRO 3.4 14.2 + - - -
337B MET* 1.3 77.6 - - - +
339B ALA* 1.3 64.1 + - - +
341B TRP* 3.2 7.1 + - - +
342B TYR* 2.9 37.0 + - - -
375B HIS* 3.6 12.4 + - - -
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLN* 3.4 13.8 + - + +
337B MET 3.1 0.4 - - - -
338B SER* 1.3 79.3 + - - +
340B PHE* 1.3 65.2 + - - +
342B TYR* 3.0 7.8 + - - +
343B ALA* 2.9 23.1 + - - +
368B ASN 4.9 3.8 - - - +
369B ALA* 4.1 20.0 - - - +
375B HIS* 3.2 40.9 + - + +
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Residues in contact with PHE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TRP* 3.7 28.7 - + - -
169B ALA* 3.2 44.6 - - + -
170B PHE* 4.1 15.3 - + + -
182B VAL* 5.2 0.4 - - + -
184B VAL* 3.8 24.0 - - + -
259B PHE* 4.2 3.4 - + - -
336B GLN 3.2 9.6 + - - +
337B MET* 3.1 20.7 + - + +
339B ALA* 1.3 78.0 - - - +
341B TRP* 1.3 104.9 + + - +
343B ALA* 3.2 2.6 + - - +
344B VAL* 3.1 31.3 + - + +
369B ALA* 4.2 17.2 - - + +
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Residues in contact with TRP 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASP* 3.0 26.6 + - - -
67B ARG* 5.2 9.6 - - - +
155B PRO* 3.6 48.0 - - + +
156B TYR* 4.0 23.3 - + + -
159B TRP* 4.6 7.6 - + + -
259B PHE* 3.7 28.5 - + + -
331B MET* 3.9 20.6 - - - -
337B MET* 2.9 40.1 + - + +
338B SER* 3.6 11.0 - - - +
340B PHE* 1.3 93.4 - + - +
342B TYR* 1.3 59.0 + - + +
344B VAL* 3.5 0.8 + - + -
345B ARG* 2.8 29.6 + - - +
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Residues in contact with TYR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU* 4.7 1.4 + - - -
46B GLU* 2.7 42.2 + - - +
67B ARG* 3.3 26.1 + - - -
338B SER* 2.9 31.8 + - - -
339B ALA* 3.0 9.0 + - - +
341B TRP* 1.3 78.4 - - + +
343B ALA* 1.3 65.9 + - - +
345B ARG* 3.2 40.2 + - + +
346B THR* 3.1 22.9 + - - -
375B HIS* 5.0 1.3 - + - -
378B TYR* 6.0 3.8 - - + -
382B ARG* 3.1 46.7 + - - +
389B PRO* 6.2 1.3 - - + -
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ALA 2.9 11.9 + - - +
340B PHE 3.2 8.5 + - - +
342B TYR* 1.3 76.4 - - - +
344B VAL* 1.3 58.6 + - + +
346B THR* 3.7 5.0 + - - -
347B ALA* 3.2 18.9 + - - +
365B ALA* 3.4 42.8 - - + +
368B ASN* 4.3 10.5 + - + +
369B ALA* 4.0 16.4 - - + +
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PRO* 3.7 20.0 - - + -
159B TRP* 4.5 17.3 - - + -
162B ILE* 4.8 4.3 - - + -
184B VAL* 4.3 13.5 - - + -
340B PHE* 3.1 42.2 + - + +
341B TRP* 4.0 3.4 - - - +
342B TYR 3.1 0.2 - - - -
343B ALA* 1.3 74.3 - - + +
345B ARG* 1.3 68.5 + - - +
346B THR 3.0 1.8 - - - -
347B ALA* 4.0 8.3 - - + -
348B VAL* 2.9 39.7 + - + +
362B LEU* 5.8 5.2 - - + -
365B ALA* 4.7 6.1 - - + -
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Residues in contact with ARG 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLN 4.2 14.3 - - - +
154B GLU* 5.1 4.7 - - - +
155B PRO* 3.7 21.7 - - + +
341B TRP 2.8 19.7 + - - +
342B TYR* 3.5 41.5 + - + +
344B VAL* 1.3 76.8 - - - +
346B THR* 1.3 82.0 + - - +
348B VAL* 4.6 1.7 - - - +
349B ILE* 3.3 34.6 + - - +
378B TYR* 5.9 5.5 - - - -
382B ARG* 5.8 2.6 - - - +
389B PRO* 3.4 30.1 + - - +
390B ASN* 3.0 25.5 + - - -
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Residues in contact with THR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TYR 3.1 5.0 + - - -
343B ALA* 3.8 9.0 - - - -
344B VAL 3.0 0.4 - - - -
345B ARG* 1.3 103.5 + - - +
347B ALA* 1.3 68.0 + - - +
348B VAL 3.2 1.6 - - - -
349B ILE* 2.9 6.2 + - - +
350B ASN* 2.8 51.1 + - - +
390B ASN* 4.6 14.8 + - - +
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 4.8 1.3 - - - -
343B ALA 3.2 17.0 + - - +
344B VAL* 3.2 8.2 + - + +
346B THR* 1.3 79.1 - - - +
348B VAL* 1.3 57.6 + - + +
350B ASN* 4.9 1.1 - - - +
351B ALA* 2.9 34.5 + - - +
361B ALA* 3.4 36.9 - - + +
362B LEU* 4.2 13.7 - - + -
365B ALA* 4.0 8.3 - - + -
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 4.0 20.6 - - + +
155B PRO* 4.9 5.4 - - + -
158B THR* 3.6 27.1 - - + +
162B ILE* 3.9 14.8 - - + -
193B LEU* 4.3 15.4 - - + +
196B LEU* 4.2 17.7 - - + -
344B VAL* 2.9 36.0 + - + +
345B ARG* 4.6 3.1 - - - +
347B ALA* 1.3 75.0 - - + +
349B ILE* 1.3 58.0 + - + +
351B ALA* 3.9 0.9 - - - +
352B ALA* 3.0 31.0 + - + +
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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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152B LEU 4.3 9.0 - - - +
153B GLN* 3.7 40.6 - - + +
345B ARG* 3.3 31.1 + - + +
346B THR* 2.9 8.0 + - - +
348B VAL* 1.3 77.7 - - + +
350B ASN* 1.3 61.6 + - - +
352B ALA* 3.2 3.2 + - - +
353B SER* 2.9 35.4 + - - -
355B ARG* 4.1 17.9 - - - +
390B ASN* 5.9 1.8 - - - +
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Residues in contact with ASN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B THR* 2.8 40.9 + - - +
347B ALA* 4.1 2.9 - - - +
349B ILE* 1.3 78.0 - - - +
351B ALA* 1.3 63.6 + - - +
353B SER* 3.9 4.3 - - - -
354B GLY 3.3 2.1 + - - -
355B ARG* 3.1 50.7 + - + -
356B GLN* 3.1 39.9 + - + +
361B ALA* 4.8 1.1 - - + -
390B ASN* 5.5 3.1 + - - +
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Residues in contact with ALA 351 (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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193B LEU* 3.9 23.1 - - + -
197B VAL* 3.2 23.3 - - + +
201B LYS* 5.4 0.2 + - - -
347B ALA 2.9 20.9 + - - +
348B VAL 4.0 2.2 - - - +
350B ASN* 1.3 76.9 - - - +
352B ALA* 1.3 60.0 + - - +
354B GLY* 4.1 4.4 + - - -
356B GLN 3.5 15.4 - - - +
358B VAL* 4.0 15.9 - - + +
361B ALA* 4.0 10.8 - - + -
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 5.7 4.5 - - + +
193B LEU* 6.1 0.2 - - + -
196B LEU* 5.6 4.9 - - + -
197B VAL* 4.2 10.9 - - + +
200B ILE* 3.5 37.2 - - + +
207B ALA* 4.0 15.0 - - + +
348B VAL* 3.0 24.2 + - + +
349B ILE* 3.2 3.8 + - - +
351B ALA* 1.3 77.2 - - - +
353B SER* 1.3 60.1 + - - +
354B GLY* 3.1 5.9 + - - -
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ALA* 4.2 14.1 - - - -
349B ILE* 2.9 21.8 + - - -
350B ASN 3.6 0.3 + - - -
352B ALA* 1.3 77.5 - - - +
354B GLY* 1.3 58.8 + - - +
355B ARG* 2.8 46.2 + - - +
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Residues in contact with GLY 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LYS* 6.1 2.7 - - - -
350B ASN 3.3 4.1 + - - -
351B ALA 4.6 4.5 - - - -
352B ALA 3.1 5.7 - - - -
353B SER* 1.3 79.5 - - - +
355B ARG* 1.3 60.8 + - - +
356B GLN* 2.9 11.8 + - - +
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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
------------------------------------------------------------
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