Contacts of the helix formed by residues 24 - 35 (chain 2) in PDB entry 3BBX
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 THR 24 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202 ALA 4.8 2.9 + - - -
212 ARG* 4.2 1.2 + - - -
222 MET 3.7 1.2 - - - -
232 ALA* 1.3 90.3 + - + +
252 LYS* 1.3 76.9 + - - +
262 ASN* 3.6 5.8 - - - +
272 GLY* 2.7 10.6 + - - -
282 ARG* 2.6 37.6 + - - +
683B U 2.9 27.8 + - - +
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Residues in contact with LYS 25 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242 THR* 1.3 87.0 - - - +
262 ASN* 1.3 80.3 + - - +
282 ARG* 3.7 4.3 + - - +
292 GLN* 3.0 30.7 + - - +
210B C 4.9 14.6 - - - +
682B G 5.0 7.8 + - - +
1367B A 5.1 12.1 + - - +
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Residues in contact with ASN 26 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 THR* 3.6 11.9 - - - +
252 LYS* 1.3 89.4 + - - +
272 GLY* 1.3 67.0 + - - +
292 GLN* 2.7 20.5 + - - +
302 VAL* 2.7 17.0 + - - +
332 ARG* 5.0 0.4 + - - +
682B G 1.9 84.2 + - - +
683B U 2.6 19.2 + - - -
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Residues in contact with GLY 27 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212 ARG* 2.8 22.7 - - - +
242 THR* 2.7 26.9 + - - -
262 ASN* 1.3 76.1 - - - +
282 ARG* 1.3 55.6 + - - -
302 VAL* 3.3 9.3 - - - +
312 LEU* 3.1 21.1 - - - +
683B U 3.3 15.5 + - - -
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Residues in contact with ARG 28 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212 ARG 2.9 7.6 + - - +
222 MET* 3.4 47.5 - - + +
242 THR 2.6 19.1 + - - +
252 LYS* 4.2 4.5 - - - +
272 GLY* 1.3 69.9 - - - -
292 GLN* 1.3 64.5 + - - +
312 LEU* 3.4 18.3 + - - +
322 ALA* 3.6 6.5 + - - +
53B A 5.5 10.7 + - - -
179B C 6.0 2.9 - - - -
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Residues in contact with GLN 29 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252 LYS 3.0 17.8 + - - +
262 ASN* 2.7 18.5 + - - +
282 ARG* 1.3 76.0 - - - +
302 VAL* 1.3 62.6 + - - +
322 ALA* 2.9 27.6 + - - +
332 ARG* 3.0 33.2 + - - +
209B C 5.5 5.3 + - - -
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Residues in contact with VAL 30 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212 ARG* 3.8 17.3 - - - +
262 ASN 2.7 17.1 + - - +
272 GLY 3.3 10.3 - - - +
292 GLN* 1.3 75.1 - - - +
312 LEU* 1.3 59.9 + - + +
332 ARG* 3.0 31.4 - - - +
342 ARG* 2.8 33.7 + - + +
466B A 3.3 39.0 - - - +
467B G 3.8 1.8 - - - +
682B G 4.3 2.0 - - - +
683B U 4.3 22.9 - - - +
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Residues in contact with LEU 31 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212 ARG* 3.3 31.2 - - + -
222 MET* 3.6 26.0 - - + -
272 GLY 3.1 21.3 - - - +
282 ARG* 3.6 13.5 - - + +
292 GLN 3.2 0.4 - - - -
302 VAL* 1.3 77.3 - - + +
322 ALA* 1.3 55.0 + - - +
342 ARG* 4.2 4.7 - - - -
352 ARG* 2.7 41.1 + - + +
422 LEU* 4.6 21.3 - - + -
442 VAL* 5.5 8.5 - - + -
466B A 5.8 0.7 - - - -
467B G 5.4 1.8 - - - +
72T GLN* 5.6 0.7 - - - +
73T ARG 5.4 3.8 - - - +
74T ILE* 5.8 4.0 - - + -
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Residues in contact with ALA 32 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282 ARG* 3.6 5.6 + - - +
292 GLN* 2.9 23.4 + - - +
312 LEU* 1.3 80.5 - - - +
332 ARG* 1.3 65.6 + - - +
342 ARG 2.9 1.9 + - - -
352 ARG* 5.2 0.4 - - - -
362 ALA* 3.0 33.9 + - + +
372 LYS* 4.9 0.7 - - - -
72T GLN* 5.3 1.1 - - - +
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Residues in contact with ARG 33 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262 ASN 5.0 0.8 + - - -
292 GLN* 3.0 33.3 + - - +
302 VAL* 3.0 42.3 - - - +
322 ALA* 1.3 76.1 - - - +
342 ARG* 1.3 56.8 + - - +
372 LYS* 2.9 52.6 - - + +
572 MG 4.1 1.9 - - - -
467B G 5.8 4.0 - - - -
468B G 5.7 0.3 + - - -
681B G 4.4 11.5 - - - +
682B G 4.5 9.7 + - - -
796B C 5.4 5.5 + - - -
797B G 3.7 43.0 + - - -
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Residues in contact with ARG 34 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302 VAL* 2.8 16.7 + - - +
312 LEU* 3.6 6.1 - - - +
322 ALA 2.9 1.2 + - - -
332 ARG* 1.3 76.3 - - - +
352 ARG* 1.3 64.3 + - - +
372 LYS 2.9 18.5 - - - +
382 GLY 3.1 7.3 - - - +
402 ALA* 3.8 12.8 - - + +
422 LEU* 3.0 13.0 - - + +
466B A 2.0 23.2 + - - -
467B G 0.7 369.7 + - - +
468B G 3.6 9.2 + - - +
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Residues in contact with ARG 35 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312 LEU* 2.7 20.3 + - + +
342 ARG* 1.3 75.8 - - - +
362 ALA* 1.3 69.6 + - - +
382 GLY 3.2 0.2 - - - +
392 ARG* 3.0 51.1 - - - +
402 ALA* 3.3 14.6 + - - +
422 LEU* 5.3 6.7 - - + +
458B G 4.5 7.5 - - - -
71T GLY* 1.6 33.2 + - - -
72T GLN* 1.0 218.2 - - + +
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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