Contacts of the helix formed by residues 272 - 284 (chain B) in PDB entry 1W45
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 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ARG* 3.5 30.3 - - - +
112B LYS* 3.1 30.8 - - - +
115B VAL* 6.1 2.2 - - - +
264B TYR 5.2 2.4 + - - +
265B ALA* 2.8 23.7 + - - +
271B THR* 1.3 73.5 + - - +
273B ASP* 1.3 67.5 + - - +
274B GLY* 3.3 21.3 - - - +
275B THR* 3.1 37.9 + - - +
276B LEU* 3.2 9.4 + - - +
278B ARG* 5.7 1.8 - - - +
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Residues in contact with ASP 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS* 3.1 39.6 + - + +
85B ARG* 3.9 20.5 + - - +
271B THR* 3.2 28.7 + - - +
272B ARG* 1.3 71.5 - - - +
274B GLY* 1.3 58.1 + - - +
276B LEU* 2.9 5.2 + - - +
277B ILE* 2.8 41.2 + - + +
311B THR* 5.0 1.0 - - - +
315B TYR* 3.0 29.2 + - + +
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ARG* 3.7 12.4 - - - +
101B GLU* 4.2 6.1 - - - +
272B ARG* 3.3 27.0 - - - +
273B ASP* 1.3 75.4 - - - +
275B THR* 1.3 60.2 + - - +
277B ILE* 4.0 5.7 - - - +
278B ARG* 3.2 37.9 + - - +
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Residues in contact with THR 275 (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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261B ARG* 3.7 40.0 + - - +
265B ALA* 3.9 7.9 - - + -
272B ARG* 3.1 33.0 + - - +
273B ASP 3.1 0.6 - - - -
274B GLY* 1.3 75.0 - - - +
276B LEU* 1.3 64.8 + - - +
278B ARG* 3.5 21.8 + - - +
279B ASN* 2.9 42.9 + - - +
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Residues in contact with LEU 276 (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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262B LEU* 3.6 25.9 - - + +
265B ALA* 4.0 9.8 - - + +
266B MET* 4.2 42.6 - - + -
271B THR* 4.5 6.1 - - + -
272B ARG 3.2 8.8 + - - +
273B ASP 2.9 7.0 + - - +
275B THR* 1.3 77.8 - - - +
277B ILE* 1.3 65.3 + - - +
280B ILE* 3.0 44.8 + - + +
303B LEU* 5.5 0.4 - - + -
307B ILE* 5.1 3.4 - - + -
311B THR* 4.5 9.0 - - + -
315B TYR* 3.6 19.7 - - - +
319B LEU* 3.9 18.4 - - + -
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Residues in contact with ILE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS* 5.0 1.3 - - + +
85B ARG* 4.2 12.6 - - + +
86B LEU* 4.0 34.8 - - + +
89B ALA* 3.7 30.1 - - + -
97B TYR* 4.0 4.0 - - - +
273B ASP* 2.8 31.1 + - + +
274B GLY* 4.0 6.7 - - - +
276B LEU* 1.3 74.6 - - - +
278B ARG* 1.3 55.2 + - - +
280B ILE* 3.7 2.0 - - - +
281B VAL* 2.8 35.9 + - + +
315B TYR* 3.3 43.3 - - + +
319B LEU* 4.7 4.3 - - + -
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 3.2 21.3 - - + +
98B GLU* 6.2 1.1 - - + -
101B GLU* 3.3 40.5 + - + +
115B VAL* 3.8 26.9 - - - +
118B GLU* 2.8 42.9 + - - +
119B ILE* 3.8 15.3 - - + +
123B ARG* 5.7 0.2 - - - +
261B ARG* 3.8 6.1 - - - +
272B ARG* 5.7 2.0 - - - +
274B GLY* 3.2 36.0 + - - +
275B THR* 3.5 24.9 + - - +
277B ILE* 1.3 79.5 - - - +
279B ASN* 1.3 57.4 + - - +
282B SER* 2.8 44.2 + - - +
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Residues in contact with ASN 279 (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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118B GLU* 3.2 33.5 + - - +
123B ARG* 5.3 0.3 + - - -
258B PHE* 3.3 35.6 - - + -
261B ARG* 4.3 11.1 - - - +
262B LEU* 3.8 23.5 - - + +
275B THR* 2.9 37.0 + - - +
278B ARG* 1.3 75.5 - - - +
280B ILE* 1.3 65.6 + - - +
282B SER* 4.2 3.7 - - - -
283B ARG* 3.1 29.4 + - + +
288B LEU* 4.9 1.6 - - - +
291B ILE* 5.1 1.0 - - - +
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Residues in contact with ILE 280 (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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86B LEU* 6.1 0.7 - - + -
262B LEU* 3.8 11.7 - - + -
276B LEU* 3.0 32.5 - - + +
277B ILE 3.1 3.0 + - - +
279B ASN* 1.3 74.7 - - - +
281B VAL* 1.3 58.1 - - + +
283B ARG 3.9 0.2 - - - -
284B SER* 2.7 34.8 + - - -
288B LEU* 3.9 27.5 - - + +
303B LEU* 4.3 9.0 - - + -
307B ILE* 4.2 7.9 - - + -
319B LEU* 4.0 22.4 - - + -
322B LEU* 4.3 21.5 - - + -
323B VAL* 3.8 28.0 - - + -
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.3 46.8 - - + +
86B LEU* 4.1 20.4 - - + -
89B ALA* 3.5 23.1 - - + +
90B LEU* 3.7 22.0 - - + -
97B TYR* 3.6 19.5 - - + +
277B ILE* 2.8 21.6 + - + +
280B ILE* 1.3 71.6 - - - +
282B SER* 1.3 64.0 + - - +
284B SER* 2.9 20.6 + - - -
322B LEU* 4.6 3.6 - - + -
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Residues in contact with SER 282 (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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10B GLN* 3.0 39.1 + - - +
11B GLU* 4.7 1.3 - - - -
97B TYR* 4.1 11.5 - - - -
98B GLU* 3.5 5.0 + - - +
118B GLU* 5.6 0.2 + - - -
123B ARG* 2.7 30.5 + - - -
278B ARG* 2.8 32.0 + - - +
279B ASN* 3.9 2.9 - - - -
281B VAL* 1.3 76.6 - - - +
283B ARG* 1.3 71.2 - - - +
286B ILE* 4.0 0.9 - - - +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B SER 5.0 2.8 + - - -
123B ARG* 4.3 19.7 - - - +
127B GLN* 4.6 11.1 + - - +
254B LEU* 4.0 13.1 - - - +
258B PHE* 3.4 38.9 - - + -
279B ASN* 3.1 21.8 - - - +
280B ILE 3.3 2.3 + - - +
281B VAL 3.2 0.4 - - - -
282B SER* 1.3 89.5 - - - +
284B SER* 1.3 65.3 - - - +
285B GLU 3.2 2.9 - - - -
286B ILE* 2.8 44.8 + - - +
287B ASP* 2.4 52.6 + - - +
288B LEU* 3.4 10.0 + - + +
291B ILE* 3.8 19.1 - - + -
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.5 1.8 - - - -
12B GLY* 2.9 34.0 + - - -
13B VAL* 3.8 20.0 + - - +
90B LEU* 5.3 0.2 - - - +
280B ILE 2.7 23.5 + - - -
281B VAL* 2.9 18.2 + - - -
283B ARG* 1.3 74.4 - - - +
285B GLU* 1.3 58.4 + - - +
286B ILE 5.2 0.2 - - - -
288B LEU* 4.2 19.0 + - - +
289B ASN* 5.6 2.8 + - - -
322B LEU* 4.4 10.7 - - - +
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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