Contacts of the helix formed by residues 269 - 283 (chain A) in PDB entry 3W7F
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 GLU 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A PHE* 3.5 34.1 + - + -
268A VAL* 1.3 76.8 - - - +
270A LYS* 1.4 69.7 + - - +
271A ARG* 3.2 6.7 - - + +
272A LYS* 3.0 18.3 + - + +
273A LYS* 2.9 20.2 + - - +
264B GLU* 5.5 6.1 - - - +
269B GLU* 5.2 2.4 - - - +
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Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.8 36.2 - - + -
268A VAL 3.7 2.2 + - - -
269A GLU* 1.4 73.7 - - - +
271A ARG* 1.3 56.1 + - - +
273A LYS* 2.8 38.0 + - + +
274A ALA* 3.0 13.2 + - - +
263B HIS* 3.2 33.5 + - - +
264B GLU* 4.6 24.5 + - - +
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A GLU* 3.2 8.4 - - + +
270A LYS* 1.3 76.5 - - - +
272A LYS* 1.3 65.1 + - - +
274A ALA* 3.1 13.4 + - - +
275A LYS* 3.0 32.4 + - - +
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLU* 3.1 34.9 + - + +
254A GLU* 5.7 3.4 + - - -
268A VAL* 3.7 19.3 - - + -
269A GLU* 3.0 20.5 + - + +
271A ARG* 1.3 80.8 - - - +
273A LYS* 1.4 54.6 + - - +
275A LYS* 3.0 29.1 + - + +
276A LEU* 2.8 45.4 + - + +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.0 20.9 + - - +
21A SER* 3.5 25.1 - - - +
24A TYR* 3.9 35.6 - - + +
243A LEU* 3.6 5.8 - - - +
247A ILE* 3.9 23.3 - - + -
268A VAL* 3.3 35.9 + - + -
269A GLU 2.9 14.3 + - - +
270A LYS* 2.8 21.8 + - - +
272A LYS* 1.4 75.5 - - - +
274A ALA* 1.3 58.7 + - - +
276A LEU* 3.3 8.7 + - - -
277A PHE* 2.8 29.3 + - - +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.4 25.3 + - + +
270A LYS 3.0 9.4 + - - +
271A ARG* 3.4 21.3 - - - +
273A LYS* 1.3 78.6 - - - +
275A LYS* 1.3 61.8 + - - +
277A PHE* 3.4 4.8 + - - +
278A HIS* 3.0 22.9 + - - +
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ARG* 3.0 24.8 + - - +
272A LYS* 3.0 34.0 + - + +
274A ALA* 1.3 75.1 - - - +
276A LEU* 1.3 68.5 + - + +
278A HIS* 2.9 16.6 + - + +
279A GLU* 2.9 40.7 + - + +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU* 4.0 9.0 - - + -
246A ARG* 4.1 22.7 - - + +
247A ILE* 4.1 34.8 - - + -
250A GLU* 4.3 20.2 - - + +
268A VAL* 4.9 1.3 - - + -
272A LYS* 2.8 38.2 + - + +
273A LYS* 3.7 7.2 - - - +
275A LYS* 1.3 77.3 - - + +
277A PHE* 1.3 64.5 + - - +
279A GLU* 3.0 30.2 + - - +
280A ILE* 3.0 17.0 + - + +
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 5.0 5.6 - - + -
28A LEU* 3.6 33.4 - - + -
239A PRO* 3.9 26.9 - - + -
240A ILE* 4.3 13.5 - - + -
243A LEU* 3.6 28.8 - - + +
273A LYS 2.8 17.3 + - - +
274A ALA* 3.7 8.1 - - - +
276A LEU* 1.3 76.5 - - - +
278A HIS* 1.3 62.7 + - - +
280A ILE* 3.3 5.8 + - + +
281A ASN* 3.0 59.5 + - - -
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Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ALA 3.0 13.7 + - - +
275A LYS* 2.9 15.1 + - + +
277A PHE* 1.3 76.5 - - - +
279A GLU* 1.3 66.7 + - + +
281A ASN* 3.5 8.5 + - - +
282A SER* 3.2 21.5 + - - -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LYS* 2.9 40.4 - - + +
276A LEU* 3.0 20.3 + - - +
278A HIS* 1.3 80.7 - - + +
280A ILE* 1.3 67.8 + - + +
282A SER* 2.9 25.9 + - - -
283A LYS* 3.6 7.1 + - - +
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PRO* 4.1 20.0 - - + +
242A GLU* 3.4 40.6 - - + +
243A LEU* 3.5 34.8 - - + +
246A ARG* 4.0 16.6 - - + -
276A LEU 3.0 14.7 + - - +
277A PHE* 3.6 7.6 - - + +
279A GLU* 1.3 75.9 - - + +
281A ASN* 1.3 64.3 + - - +
282A SER 3.1 1.0 + - - -
283A LYS* 3.1 25.0 + - - +
284A TYR* 3.3 28.2 + - + +
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Residues in contact with ASN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PRO* 3.7 24.4 - - - +
277A PHE* 3.0 58.3 + - - +
278A HIS* 3.9 8.1 - - - +
279A GLU 3.2 0.2 - - - -
280A ILE* 1.3 72.3 - - - +
282A SER* 1.3 65.3 + - - +
284A TYR* 3.1 28.6 + - + +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A HIS* 3.2 14.7 + - - -
279A GLU* 2.9 21.5 + - - -
281A ASN* 1.3 80.5 - - - +
283A LYS* 1.3 61.0 + - - +
284A TYR 3.4 2.8 + - - -
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A GLU* 2.5 36.8 + - - -
246A ARG* 5.1 11.0 - - - +
279A GLU 4.0 5.6 - - - +
280A ILE* 3.3 22.4 + - - +
282A SER* 1.3 80.1 + - - +
284A TYR* 1.3 67.3 + - + +
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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