Contacts of the helix formed by residues 323 - 339 (chain B) in PDB entry 3LRB
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 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B LEU* 6.5 0.4 - - + -
298B GLY* 4.5 9.2 - - - +
299B GLN* 5.8 4.3 - - - +
302B LYS* 3.5 28.5 - - + -
315B ALA 3.4 24.9 - - - +
317B VAL* 4.0 8.5 - - + -
322B THR* 1.3 85.4 - - + +
324B VAL* 1.3 58.7 + - - +
325B ALA 3.0 2.9 - - - -
326B GLY 2.5 27.7 + - - +
327B LEU* 3.1 39.8 - - + +
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 3.2 35.6 - - + +
317B VAL* 4.7 0.2 - - - +
318B ASN* 3.8 46.8 - - + +
322B THR* 3.7 8.7 + - - +
323B PRO* 1.3 71.0 - - - +
325B ALA* 1.3 69.1 + - + +
327B LEU* 3.8 0.6 + - - -
328B ILE* 3.2 39.6 + - + +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 5.5 2.7 - - + -
314B PHE* 4.7 6.5 - - + +
315B ALA 4.1 1.8 - - - +
316B ARG* 3.9 31.1 - - + +
317B VAL 5.3 0.4 - - - +
323B PRO 2.8 3.6 + - - -
324B VAL* 1.3 83.4 - - + +
326B GLY* 1.3 56.6 + - - +
328B ILE* 3.5 6.6 + - - +
329B ILE* 2.7 41.5 + - + +
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Residues in contact with GLY 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LYS* 3.4 30.9 + - - -
314B PHE* 3.8 12.7 - - - +
323B PRO* 2.5 17.9 + - - +
325B ALA* 1.3 72.5 - - - +
327B LEU* 1.3 53.1 + - - -
329B ILE* 2.6 29.8 + - - +
330B VAL* 3.0 10.7 + - - +
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Residues in contact with LEU 327 (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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137B VAL* 3.6 26.9 - - + +
140B ASN* 3.0 48.9 - - + +
141B ILE* 4.3 6.5 - - + +
294B THR* 4.6 15.5 - - - +
295B LEU* 5.3 3.8 - - + -
298B GLY* 4.7 11.9 - - - -
302B LYS* 4.5 0.4 - - - +
322B THR* 5.5 0.7 - - + -
323B PRO* 3.1 48.9 + - + +
324B VAL* 4.6 1.1 - - - +
326B GLY* 1.3 71.5 - - - +
328B ILE* 1.3 57.2 + - - +
330B VAL* 3.1 15.3 + - + +
331B GLY 2.8 23.7 + - - -
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TRP* 3.8 17.1 - - + -
137B VAL* 4.3 4.0 - - - -
138B LEU* 5.9 1.6 - - + -
141B ILE* 3.9 20.6 - - + -
324B VAL* 3.2 39.1 + - + +
325B ALA* 3.7 6.1 - - - +
326B GLY 3.1 0.8 - - - -
327B LEU* 1.3 77.6 - - - +
329B ILE* 1.3 58.4 + - + +
331B GLY 3.5 0.7 + - - -
332B ILE* 3.0 37.5 + - + +
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Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 5.9 5.8 - - + -
313B ILE* 4.3 24.2 - - + -
314B PHE* 4.6 17.7 - - + -
325B ALA* 2.7 31.2 - - + +
326B GLY* 2.6 14.3 + - - +
328B ILE* 1.3 72.0 - - + +
330B VAL* 1.3 58.9 + - + +
331B GLY 3.1 1.6 - - - -
332B ILE* 4.1 13.2 - - + -
333B LEU* 3.0 43.2 + - + +
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 4.1 26.5 - - + +
98B TRP* 3.8 22.0 - - + -
137B VAL* 5.3 0.9 - - + -
294B THR* 5.1 10.8 - - - +
297B ALA* 4.5 13.9 - - + +
302B LYS* 4.2 8.5 - - - +
326B GLY 3.0 12.0 + - - +
327B LEU* 3.4 14.8 - - + +
329B ILE* 1.3 77.4 - - + +
331B GLY* 1.3 51.5 + - - +
333B LEU* 4.3 4.7 - - - -
334B MET* 2.7 65.9 + - + +
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Residues in contact with GLY 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TRP* 3.2 26.7 - - - -
137B VAL* 3.9 12.7 - - - +
327B LEU 2.8 12.5 + - - -
328B ILE 3.5 0.6 + - - -
329B ILE 3.1 0.6 - - - -
330B VAL* 1.3 75.5 - - - +
332B ILE* 1.3 66.9 + - - +
334B MET* 3.7 3.9 - - - +
335B THR* 2.8 28.8 + - - -
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TRP* 3.3 13.6 - - + -
328B ILE* 3.0 28.5 + - + +
329B ILE* 4.0 18.8 - - + +
331B GLY* 1.3 73.7 - - - +
333B LEU* 1.3 66.5 + - + +
335B THR* 3.3 4.2 - - - -
336B ILE* 3.0 41.3 + - + +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 5.2 7.0 - - + -
98B TRP* 3.3 45.5 - - + +
329B ILE* 3.0 28.5 + - + +
330B VAL* 3.9 5.2 - - - +
332B ILE* 1.3 78.1 - - + +
334B MET* 1.3 68.2 + - - +
336B ILE* 3.0 30.5 + - + +
337B PHE* 3.3 11.9 + - + +
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Residues in contact with MET 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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98B TRP* 4.1 15.2 - - + +
101B ASN* 3.7 32.1 - - + -
102B ILE* 3.3 27.3 - - + +
133B LEU* 3.7 32.8 - - + +
137B VAL* 3.8 21.8 - - + -
294B THR* 4.6 6.7 - - + -
330B VAL* 2.7 57.8 + - + +
331B GLY* 3.7 3.1 - - - +
333B LEU* 1.3 72.1 - - - +
335B THR* 1.3 66.8 + - - +
338B GLN* 2.9 19.8 + - - +
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Residues in contact with THR 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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130B VAL* 3.4 16.2 - - + +
133B LEU* 4.4 3.6 - - - +
134B TRP* 3.0 24.0 + - - +
331B GLY 2.8 18.7 + - - -
332B ILE* 3.3 9.9 - - - -
333B LEU 3.0 0.4 + - - -
334B MET* 1.3 75.3 - - - +
336B ILE* 1.3 58.6 + - + +
337B PHE 2.6 2.6 + - - -
338B GLN* 2.2 41.9 + - - +
339B LEU* 3.1 33.6 + - + -
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Residues in contact with ILE 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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332B ILE* 3.0 39.0 - - + +
333B LEU* 3.0 23.5 + - + +
335B THR* 1.3 78.2 - - + +
337B PHE* 1.3 61.1 + - - +
339B LEU* 3.9 13.7 + - + +
340B SER* 3.1 19.7 + - - +
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Residues in contact with PHE 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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98B TRP* 5.1 4.7 - - + +
99B ILE* 4.9 15.9 - - + -
102B ILE* 3.0 50.9 - - + -
103B ALA* 5.7 3.4 - - + -
333B LEU* 3.3 8.1 + - + +
334B MET 4.1 0.4 - - - +
335B THR 2.6 6.3 + - - -
336B ILE* 1.3 73.6 - - - +
338B GLN* 1.3 53.7 + - - +
339B LEU 2.6 14.2 + - - -
340B SER* 2.7 23.0 + - - -
341B SER* 3.0 20.4 + - - -
345B ASN* 2.9 35.4 - - - -
353B VAL* 4.2 23.6 - - + -
354B SER* 5.9 1.6 - - - -
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Residues in contact with GLN 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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102B ILE* 3.6 28.6 + - + +
105B VAL* 3.4 10.3 - - - +
106B VAL* 3.9 10.3 - - - +
126B THR* 4.7 5.5 + - - +
129B CYS* 2.9 47.4 - - - +
130B VAL* 4.1 13.9 - - + +
133B LEU* 3.2 25.1 - - + -
334B MET 2.9 12.9 + - - +
335B THR* 2.2 28.5 + - - +
337B PHE* 1.3 70.2 - - - +
339B LEU* 1.3 54.6 + - - +
340B SER 3.5 2.1 + - - -
341B SER 3.5 15.3 - - - +
342B ILE* 3.6 4.9 + - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B THR* 4.2 6.1 - - - +
127B ILE* 5.9 7.2 - - + -
130B VAL* 3.4 20.9 - - + -
335B THR* 3.4 33.7 - - + +
336B ILE* 4.0 11.2 - - + +
337B PHE 2.6 4.0 + - - -
338B GLN* 1.3 72.7 - - - +
340B SER* 1.3 67.4 + - - +
342B ILE* 3.3 27.6 - - + +
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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