Contacts of the helix formed by residues 271 - 285 (chain B) in PDB entry 4DQ6
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 ASN 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLY 3.1 15.9 - - - +
242A LEU* 4.2 1.8 - - - +
243A GLN* 3.7 24.9 + - + +
271A ASN* 3.5 30.5 - - - +
92B TYR* 4.6 2.0 + - - -
242B LEU* 2.8 28.6 + - - +
243B GLN* 4.2 5.5 + - - +
269B ARG 3.8 0.2 + - - -
270B ASN* 1.3 77.8 - - - +
272B CYS* 1.3 66.9 + - - +
273B PHE* 2.9 14.7 + - - +
274B SER* 2.8 30.2 + - - -
275B LEU* 3.1 16.3 + - - +
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Residues in contact with CYS 272 (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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241A GLY* 2.8 16.1 + - - +
242A LEU* 3.7 29.2 - - - -
54B ARG* 3.6 43.6 + - - +
60B TYR* 4.1 11.9 - - - -
63B THR* 3.3 26.9 + - + +
271B ASN* 1.3 74.5 - - - +
273B PHE* 1.3 74.0 + - - +
275B LEU* 3.8 4.8 + - - +
276B VAL* 3.8 14.4 + - - +
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Residues in contact with PHE 273 (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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51A LEU* 4.4 11.4 - - + -
55A LEU* 5.2 0.2 - - + -
242A LEU* 3.7 25.8 - - + -
273A PHE* 3.5 40.8 - + + -
51B LEU* 3.6 45.2 - - + +
54B ARG* 4.0 13.0 - - + -
55B LEU* 3.7 23.8 - - + -
60B TYR* 4.1 20.4 - + - -
242B LEU* 4.6 4.3 - - + -
271B ASN* 2.9 7.8 + - - +
272B CYS* 1.3 85.7 - - - +
274B SER* 1.3 66.5 + - - +
275B LEU 3.2 1.3 - - - -
276B VAL* 3.3 4.7 + - - +
277B ALA* 3.0 26.1 + - - +
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.4 35.4 - - - +
243B GLN 2.9 14.9 + - - -
244B SER* 3.3 7.7 - - - -
270B ASN* 2.9 20.9 + - - +
271B ASN* 2.8 24.1 + - - -
273B PHE* 1.3 73.2 - - - +
275B LEU* 1.3 63.7 + - - +
277B ALA* 4.2 1.5 - - - +
278B THR* 2.8 31.9 + - - -
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Residues in contact with LEU 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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15A PHE* 3.6 34.1 - - + -
63B THR* 3.7 13.2 - - + -
64B THR 3.4 28.0 - - - +
65B ARG* 3.9 13.2 - - + -
66B PRO* 3.7 8.1 - - + -
69B TYR* 3.5 31.8 - - + -
270B ASN* 3.8 21.9 - - + +
271B ASN 3.1 13.9 + - - +
272B CYS 3.9 5.4 - - - +
273B PHE 3.2 0.2 - - - -
274B SER* 1.3 82.4 + - - +
276B VAL* 1.3 64.2 + - + +
279B GLU* 3.5 17.5 + - - +
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.7 37.7 - - + -
50B SER* 3.5 35.5 + - - +
51B LEU* 4.2 5.6 - - + +
53B ASN* 6.1 0.9 - - - +
54B ARG* 3.9 17.9 - - + -
272B CYS 3.8 12.3 + - - +
273B PHE* 3.6 9.6 - - - +
275B LEU* 1.3 79.0 - - + +
277B ALA* 1.3 64.0 + - - +
279B GLU* 3.6 5.6 + - - +
280B ALA* 3.0 30.1 + - - +
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Residues in contact with ALA 277 (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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47B ILE* 3.9 18.4 - - + +
50B SER* 3.5 11.2 - - - +
51B LEU* 4.2 3.6 - - + -
239B ILE* 4.2 6.6 - - + +
242B LEU* 3.4 32.8 - - + -
273B PHE 3.0 12.3 + - - +
274B SER 4.2 1.8 - - - +
276B VAL* 1.3 76.6 - - - +
278B THR* 1.3 58.4 + - - +
280B ALA* 3.9 1.0 - - - +
281B SER* 2.9 32.2 + - - -
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Residues in contact with THR 278 (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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69B TYR* 3.6 29.3 - - + +
72B SER* 4.9 1.1 - - - +
73B ILE* 4.7 7.6 - - + -
233B PRO* 3.8 17.6 - - + +
239B ILE* 4.9 1.6 - - - +
244B SER* 2.7 29.5 + - - +
246B TYR* 5.7 0.7 - - + -
274B SER* 2.8 21.3 + - - -
277B ALA* 1.3 75.5 - - - +
279B GLU* 1.3 63.4 + - - +
281B SER* 2.8 22.2 + - - -
282B TYR* 3.2 25.3 + - + -
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 5.9 2.0 - - - -
66B PRO* 4.7 3.1 - - - +
68B SER* 2.7 38.8 + - - -
69B TYR* 3.2 18.2 + - - +
72B SER* 3.6 19.0 - - - +
275B LEU* 3.5 11.1 + - - +
276B VAL* 3.9 7.2 - - - +
277B ALA 3.4 0.4 - - - -
278B THR* 1.3 79.9 - - - +
280B ALA* 1.3 57.5 + - - +
283B ASN* 2.9 54.2 + - - +
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Residues in contact with ALA 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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46B CYS* 3.7 16.7 - - - +
47B ILE* 4.5 1.1 - - - -
50B SER* 3.5 26.9 - - - +
276B VAL 3.0 19.9 + - - +
277B ALA* 3.9 2.7 - - - +
279B GLU* 1.3 76.6 - - - +
281B SER* 1.3 58.8 + - - +
283B ASN* 4.9 0.2 - - - -
284B ASN* 2.8 46.5 + - - +
285B GLY 3.6 1.0 + - - -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.9 17.4 - - - +
76B TRP* 4.4 0.2 - - - -
233B PRO* 3.6 18.6 - - - +
237B PHE* 3.3 37.8 - - - -
239B ILE* 4.7 1.3 - - - -
277B ALA 2.9 16.4 + - - -
278B THR 2.8 20.1 + - - -
280B ALA* 1.3 76.5 - - - +
282B TYR* 1.3 61.7 + - - +
285B GLY* 2.9 29.8 + - - +
286B GLU 4.3 0.2 + - - -
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Residues in contact with TYR 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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72B SER* 3.8 20.9 - - - +
73B ILE* 3.9 25.4 - - + -
76B TRP* 3.3 50.2 - + + -
79B ARG* 2.7 32.6 + - - -
205B ASP* 4.3 5.3 + - - -
232B ALA 3.2 25.8 + - - -
233B PRO* 3.9 15.5 - - + -
237B PHE* 4.0 17.3 - + - -
246B TYR* 2.9 37.7 + + - -
278B THR* 3.2 21.0 + - + +
281B SER* 1.3 78.4 + - - +
283B ASN* 1.3 59.0 + - - +
285B GLY 4.5 0.7 + - - -
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Residues in contact with ASN 283 (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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68B SER* 5.0 1.4 + - - -
72B SER* 3.4 23.2 - - - +
75B ASN* 5.3 5.0 + - - +
79B ARG* 4.1 12.6 + - - +
279B GLU* 2.9 44.5 + - - +
280B ALA* 4.9 0.2 - - - -
282B TYR* 1.3 80.5 - - - +
284B ASN* 1.3 74.3 + - - +
286B GLU* 6.0 0.5 - - - +
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Residues in contact with ASN 284 (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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46B CYS* 3.7 24.2 - - + +
280B ALA* 2.8 26.4 + - - +
283B ASN* 1.3 90.1 + - - +
285B GLY* 1.3 61.6 + - - +
286B GLU 3.4 4.0 + - - -
287B SER* 4.5 6.2 + - - -
288B TRP* 5.3 0.5 + - - +
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Residues in contact with GLY 285 (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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46B CYS* 3.8 14.1 - - - -
237B PHE* 3.5 21.0 - - - -
280B ALA 3.6 1.4 + - - -
281B SER 2.9 19.5 + - - -
282B TYR 4.5 0.2 + - - -
284B ASN* 1.3 75.5 - - - +
286B GLU* 1.3 59.1 + - - +
287B SER 3.3 2.5 - - - -
288B TRP* 3.1 9.7 + - - +
289B LEU* 2.9 24.1 + - - +
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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