Contacts of the helix formed by residues 327 - 342 (chain B) in PDB entry 2BYL
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 PRO 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLN* 3.8 11.0 - - - +
108B LEU* 3.7 35.4 - - + +
109B THR 3.5 17.9 - - - +
110B LEU* 4.1 4.7 - - - +
111B THR 4.7 2.9 - - - +
117B ASN* 3.7 31.4 - - + +
119B VAL* 3.8 21.9 - - + +
325B GLY 3.7 0.2 - - - -
326B ASN* 1.3 84.2 - - + +
328B LEU* 1.3 61.0 + - - +
330B CYS* 3.4 2.5 + - + +
331B ARG* 3.1 28.9 + - - +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.2 11.9 - - + -
298A LEU 3.4 24.9 - - - +
101B LEU* 3.4 49.8 - - + +
104B GLN* 3.8 21.5 - - + +
105B VAL* 3.9 6.5 - - + +
109B THR* 4.0 32.3 - - + +
299B TYR* 3.9 8.1 - - + -
326B ASN* 3.0 9.0 + - - +
327B PRO* 1.3 80.0 - - - +
329B GLY* 1.3 63.3 + - - +
331B ARG* 3.4 1.7 + - - +
332B VAL* 3.1 28.4 + - - +
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Residues in contact with GLY 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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299B TYR* 3.8 29.2 - - - -
301B VAL* 3.7 13.1 - - - +
326B ASN* 2.8 16.3 + - - -
328B LEU* 1.3 76.7 - - - +
330B CYS* 1.3 55.1 + - - +
332B VAL* 3.3 5.8 + - - +
333B ALA* 2.9 29.5 + - - +
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Residues in contact with CYS 330 (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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119B VAL* 3.6 20.4 - - + -
120B LEU* 3.6 37.7 - - - -
123B TYR* 3.8 25.3 - - + -
138B PRO* 5.9 0.2 - - - -
301B VAL* 5.9 1.3 - - - -
325B GLY* 3.7 10.5 - - - -
326B ASN 3.1 21.9 + - - +
327B PRO 3.8 0.4 - - - +
328B LEU 3.3 0.2 - - - -
329B GLY* 1.3 71.5 - - - +
331B ARG* 1.3 60.8 + - - +
333B ALA* 3.4 3.6 + - - +
334B ILE* 3.0 34.7 + - - +
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ALA* 3.7 30.3 - - + +
104B GLN* 3.3 32.1 + - + +
107B LYS* 5.5 6.5 - - - +
118B ASN* 4.3 9.7 + - - -
119B VAL* 3.7 30.2 - - + +
122B GLU* 3.3 34.3 + - - -
327B PRO 3.1 18.9 + - - +
328B LEU 3.8 3.8 - - - +
330B CYS* 1.3 76.2 - - - +
332B VAL* 1.3 63.2 + - - +
334B ILE* 3.5 11.4 + - - +
335B ALA 3.3 16.8 + - - -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 3.8 17.1 - - + +
100B ALA* 4.6 3.6 - - - -
101B LEU* 3.4 43.5 - - + +
295B SER* 3.7 30.5 - - - +
298B LEU* 4.4 4.3 - - + -
299B TYR* 3.8 15.0 - - + -
301B VAL* 4.8 0.2 - - + -
328B LEU 3.1 16.9 + - - +
329B GLY 3.3 8.7 + - - +
330B CYS 3.3 0.2 - - - -
331B ARG* 1.3 76.2 - - - +
333B ALA* 1.3 58.9 + - - +
335B ALA* 3.3 2.9 + - - +
336B ALA* 2.9 29.3 + - - +
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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
----------------------------------------------------------
123B TYR* 3.5 25.8 - - + -
294B LEU* 3.3 22.2 - - + +
301B VAL* 4.1 17.5 - - + -
329B GLY 2.9 17.3 + - - +
330B CYS* 3.4 2.7 + - - +
332B VAL* 1.3 74.3 - - - +
334B ILE* 1.3 65.0 + - - +
336B ALA* 3.7 0.5 - - - +
337B LEU* 3.0 31.3 + - - +
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 4.8 2.7 - - + -
122B GLU* 4.2 24.2 - - + +
123B TYR* 3.8 39.7 - - + +
126B TYR* 4.4 22.6 + - + -
330B CYS 3.0 24.0 + - - +
331B ARG* 3.9 17.0 - - - +
333B ALA* 1.3 75.7 - - - +
335B ALA* 1.3 58.4 + - - +
337B LEU* 3.4 2.3 + - - +
338B GLU* 3.0 55.0 + - + +
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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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96B LYS* 3.5 23.4 - - + +
97B ILE* 4.0 9.4 - - - -
100B ALA* 3.8 20.6 - - + -
331B ARG 3.3 13.9 + - - +
332B VAL 3.7 3.8 - - - +
333B ALA 3.3 0.2 - - - -
334B ILE* 1.3 76.9 - - - +
336B ALA* 1.3 65.5 + - - +
338B GLU* 3.3 12.2 + - - +
339B VAL* 3.0 28.1 + - - +
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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
----------------------------------------------------------
90B GLN* 3.2 30.0 + - - +
97B ILE* 3.7 15.4 - - + +
294B LEU 3.2 25.4 - - - +
295B SER 3.7 15.0 - - - -
296B GLY 3.7 0.2 - - - +
332B VAL 2.9 15.2 + - - +
333B ALA 3.7 0.2 - - - +
335B ALA* 1.3 76.8 - - - +
337B LEU* 1.3 63.9 + - + +
339B VAL* 3.5 2.3 + - - +
340B LEU* 3.4 15.0 + - - +
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 4.4 6.7 - - + -
126B TYR* 3.7 33.8 + - + +
127B ILE* 4.1 21.1 - - + -
130B LEU* 4.3 9.9 - - + -
131B PHE* 4.5 3.4 - - + -
269B LEU* 3.8 30.1 - - + -
275B TRP* 3.7 18.4 - - + -
294B LEU* 3.9 25.8 - - + +
333B ALA 3.0 20.6 + - - +
336B ALA* 1.3 76.0 - - - +
338B GLU* 1.3 66.1 + - - +
340B LEU* 3.2 10.0 + - + +
341B GLU* 3.2 18.4 + - - +
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LYS* 3.0 36.6 + - - +
126B TYR* 3.4 26.0 + - + +
334B ILE* 3.0 36.1 + - - +
335B ALA* 3.7 4.6 - - - +
337B LEU* 1.3 76.6 - - - +
339B VAL* 1.3 56.3 + - - +
341B GLU* 3.4 5.0 + - - +
342B GLU* 2.8 40.5 + - + +
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLN* 3.7 22.0 - - + -
94B HIS* 3.5 41.5 - - + +
96B LYS* 3.5 21.1 - - + +
97B ILE* 4.2 7.0 - - + -
335B ALA 3.0 19.1 + - - +
336B ALA 3.6 8.3 - - - +
337B LEU 3.3 0.2 - - - -
338B GLU* 1.3 76.1 - - - +
340B LEU* 1.3 64.4 + - - +
342B GLU* 4.5 5.6 - - - +
343B GLU* 3.0 36.0 + - - +
345B LEU* 4.2 6.9 - - + +
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Residues in contact with LEU 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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89B ASN* 4.4 7.0 - - + -
90B GLN* 3.7 26.0 - - + +
269B LEU* 3.6 48.0 - - + +
270B ALA* 4.0 11.4 - - + +
275B TRP* 3.8 24.2 - - + -
336B ALA 3.4 12.1 + - - +
337B LEU* 3.2 13.7 + - + +
339B VAL* 1.3 76.4 - - - +
341B GLU* 1.3 62.4 + - - +
344B ASN* 3.4 2.9 + - - -
345B LEU* 3.3 46.7 + - + +
346B ALA 4.7 1.6 + - - -
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Residues in contact with GLU 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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126B TYR* 5.0 5.2 + - - +
130B LEU* 4.1 12.5 - - - +
275B TRP* 3.7 31.6 + - + -
337B LEU 3.2 9.3 + - - +
338B GLU* 3.5 11.2 - - - +
340B LEU* 1.3 77.2 - - - +
342B GLU* 1.3 69.4 + - + +
344B ASN* 3.2 24.4 + - - +
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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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96B LYS* 2.6 33.0 + - - +
338B GLU* 2.8 27.5 + - + +
339B VAL* 4.1 4.3 - - - +
341B GLU* 1.3 78.8 - - + +
343B GLU* 1.3 67.0 + - + +
344B ASN* 3.5 10.0 + - - -
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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
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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