Contacts of the helix formed by residues 280 - 291 (chain B) in PDB entry 3THY
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 ARG 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 3.8 29.9 - - - -
63A VAL* 3.8 21.8 + - - +
65A LYS* 5.9 3.4 - - - +
79A VAL 5.5 1.0 + - - -
84A ASN* 5.3 1.8 - - - +
276B ILE* 4.3 0.9 - - + -
277B PRO* 2.8 29.6 + - + +
279B HIS* 1.3 107.6 - - - +
281B LEU* 1.3 68.5 + - - +
282B PHE* 3.5 6.8 - - - -
283B VAL* 3.5 18.0 + - - +
284B HIS* 3.2 44.7 + - + +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B CYS* 4.5 10.5 - - + -
247B TYR* 3.7 47.8 - - + +
276B ILE* 4.0 13.0 - - + -
277B PRO 3.8 0.6 + - - -
278B THR 3.0 17.7 + - - +
279B HIS 3.5 0.8 - - - -
280B ARG* 1.3 78.6 - - - +
282B PHE* 1.3 65.8 + - - +
283B VAL 3.0 1.0 + - - -
284B HIS* 3.0 1.0 + - - +
285B VAL* 2.9 49.0 + - + +
297B VAL* 4.3 10.8 - - + -
299B LYS* 5.1 0.2 - - - -
334B ASP* 4.1 34.1 - - + +
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.4 22.0 - - + -
62A GLY* 3.6 24.9 - - - -
63A VAL* 4.7 0.7 - - + -
278B THR 5.8 0.2 - - - -
279B HIS 3.8 22.4 - - - -
280B ARG* 4.6 2.2 - - - -
281B LEU* 1.3 78.7 - - - +
283B VAL* 1.3 89.5 + - + +
285B VAL* 4.5 2.9 - - - -
286B ARG* 3.0 31.6 + - - +
333B GLU 5.4 0.9 - - - +
334B ASP 3.4 21.5 + - - +
335B VAL* 3.6 18.8 - - - +
337B PRO* 3.3 36.6 - - + -
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.7 36.6 - - + +
60A THR* 4.1 5.6 - - + -
63A VAL* 3.4 16.6 - - + -
280B ARG* 3.5 25.8 + - - +
281B LEU 3.0 0.8 + - - -
282B PHE* 1.3 116.0 - - + +
284B HIS* 1.3 66.7 + - + +
286B ARG* 3.2 1.9 + - - +
287B ARG* 3.0 41.2 + - - +
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Residues in contact with HIS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 5.9 1.3 - - - -
249B PHE* 5.2 2.7 - - + -
261B LEU* 3.5 32.8 - - + +
263B ILE* 4.5 11.2 - - + -
276B ILE* 3.5 41.9 - - + +
277B PRO* 6.2 0.2 - - - +
280B ARG* 3.2 42.0 + - + +
281B LEU 3.0 2.4 + - - -
283B VAL* 1.3 84.8 - - + +
285B VAL* 1.3 62.6 + - - +
287B ARG* 3.6 33.4 + - - +
288B LEU* 3.2 28.6 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B CYS* 4.6 5.4 - - - -
281B LEU* 2.9 45.6 + - + +
282B PHE 4.0 3.4 - - - +
284B HIS* 1.3 78.3 - - + +
286B ARG* 1.3 60.8 + - - +
288B LEU* 3.3 5.4 + - - +
289B VAL* 2.8 46.9 + - + +
295B VAL* 4.3 20.8 - - + +
297B VAL* 4.6 7.2 - - + -
325B TYR* 4.3 15.5 - - + -
334B ASP* 6.6 0.2 - - + -
335B VAL* 3.8 24.0 - - + -
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE 4.8 1.1 - - - +
59A LYS* 3.6 26.5 + - + +
60A THR* 3.6 18.5 - - - -
282B PHE* 3.0 21.1 + - - +
283B VAL 3.8 2.5 - - - +
285B VAL* 1.3 73.2 - - - +
287B ARG* 1.3 65.4 + - - +
289B VAL* 3.9 8.0 - - - +
290B ALA* 3.1 24.6 + - - +
330B LEU* 4.1 24.4 - - + +
335B VAL* 2.9 40.2 + - + +
336B ASN* 2.9 28.3 + - - +
337B PRO* 5.6 1.1 - - - -
348B ASP* 3.2 38.4 + - - +
349B GLU 4.5 2.4 + - - -
350B ILE* 6.1 0.2 - - - +
351B MET* 4.4 8.6 - - - +
614B ARG* 4.5 4.4 - - - +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.2 35.6 + - - +
58A PHE* 3.4 20.5 - - - +
59A LYS* 4.3 9.0 + - + +
84A ASN* 3.2 29.0 + - - +
260B GLU 4.0 6.3 + - - +
261B LEU* 3.1 50.3 + - + +
262B ASN* 3.7 10.7 + - - -
283B VAL* 3.0 35.4 + - - +
284B HIS* 3.6 22.5 + - - +
285B VAL 3.2 0.2 - - - -
286B ARG* 1.3 78.9 - - - +
288B LEU* 1.3 61.3 + - - +
290B ALA* 3.5 3.5 + - - +
291B LYS* 3.4 27.9 + - - +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 3.9 29.6 - - + -
240B CYS* 5.7 0.4 - - - -
249B PHE* 4.3 17.9 - - + -
256B ILE* 4.4 7.9 - - + +
257B ALA* 5.3 2.7 - - - -
260B GLU* 3.9 24.9 - - + -
261B LEU* 4.0 12.6 - - + -
284B HIS 3.2 17.7 + - - +
285B VAL* 3.7 4.0 - - - +
287B ARG* 1.3 79.5 - - - +
289B VAL* 1.3 64.2 + - - +
291B LYS* 3.1 12.2 + - - +
293B TYR* 3.2 43.1 + - + +
295B VAL* 3.7 20.6 - - + -
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 2.8 24.6 + - + +
286B ARG* 3.9 7.0 - - - +
288B LEU* 1.3 75.6 - - - +
290B ALA* 1.3 62.0 + - - +
292B GLY* 3.2 12.1 + - - -
293B TYR 3.7 7.5 - - - +
295B VAL* 4.2 6.1 - - + -
325B TYR* 3.9 36.8 - - + +
326B THR 3.3 31.0 - - - +
327B LYS* 3.5 20.1 + - + +
330B LEU* 4.0 21.3 - - + -
351B MET* 4.6 2.7 - - + -
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LYS* 4.2 22.0 - - + +
286B ARG 3.1 17.6 + - - +
287B ARG 3.7 6.1 - - - +
288B LEU 3.1 0.2 - - - -
289B VAL* 1.3 74.0 - - - +
291B LYS* 1.3 62.6 + - + +
292B GLY 3.0 6.1 + - - -
327B LYS* 3.2 24.4 + - - +
351B MET* 3.9 24.4 - - + +
440B GLN 4.1 3.6 - - - +
441B ASP 3.6 13.7 - - - +
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Residues in contact with LYS 291 (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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59A LYS* 4.7 15.2 - - - +
260B GLU* 3.4 42.1 + - + +
287B ARG* 3.5 16.4 - - - +
288B LEU* 3.1 2.8 + - - +
290B ALA* 1.3 78.4 - - + +
292B GLY* 1.3 58.0 + - - +
293B TYR* 3.4 29.3 - - + -
327B LYS* 4.5 2.1 + - - -
440B GLN* 4.8 20.1 + - + +
443B ARG* 6.0 1.4 - - - +
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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