Contacts of the helix formed by residues 269 - 282 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLU* 5.0 12.5 - - + +
267A PHE* 4.4 20.8 - - - -
269A GLU* 5.2 2.3 - - - +
254B GLU* 5.7 0.2 + - - -
267B PHE* 4.3 20.1 - - + +
268B VAL* 1.4 78.2 - - - +
270B LYS* 1.3 70.5 + - - +
271B ARG* 4.1 13.7 - - + +
272B LYS* 2.8 20.9 + - + +
273B LYS* 3.1 12.1 + - - +
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Residues in contact with LYS 270 (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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178A GLU* 5.1 8.5 + - - -
263A HIS* 3.4 30.1 + - + +
264A GLU* 5.1 14.3 - - + +
24B TYR* 4.1 30.9 - - + -
268B VAL 4.0 0.8 + - - -
269B GLU* 1.3 74.1 - - - +
271B ARG* 1.3 65.0 + - - +
273B LYS* 3.1 19.1 + - + +
274B ALA* 3.1 21.0 + - + +
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Residues in contact with ARG 271 (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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264A GLU* 6.2 0.8 - - - +
269B GLU* 3.0 13.5 - - + +
270B LYS* 1.3 79.8 - - - +
272B LYS* 1.3 58.0 + - - +
274B ALA* 3.3 11.0 + - - +
275B LYS* 3.0 42.0 + - + +
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Residues in contact with LYS 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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250B GLU* 3.9 28.1 + - + -
254B GLU* 5.3 6.1 - - - +
268B VAL* 3.6 16.6 - - + -
269B GLU* 2.8 21.5 + - + +
271B ARG* 1.3 73.3 - - - +
273B LYS* 1.3 55.6 + - - +
275B LYS* 2.8 27.8 + - + +
276B LEU* 2.6 61.4 + - + +
279B GLU* 5.0 2.2 + - - -
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Residues in contact with LYS 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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20B LYS* 3.0 28.3 + - - +
21B SER* 4.0 14.7 + - - +
24B TYR* 3.8 37.5 - - + +
243B LEU* 3.5 6.3 - - - +
247B ILE* 3.8 22.0 - - + -
268B VAL* 3.6 34.5 + - + -
269B GLU 3.1 9.1 + - - +
270B LYS* 3.5 17.8 - - - +
272B LYS* 1.3 75.4 - - - +
274B ALA* 1.3 58.2 + - - +
276B LEU* 3.3 9.8 + - - -
277B PHE* 2.8 28.8 + - - +
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Residues in contact with ALA 274 (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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24B TYR* 3.3 23.4 + - + +
270B LYS* 3.1 11.6 + - + +
271B ARG* 3.5 18.6 - - - +
272B LYS 3.1 0.6 - - - -
273B LYS* 1.3 74.3 - - - +
275B LYS* 1.3 66.0 + - - +
277B PHE* 3.1 3.6 + - - +
278B HIS* 2.9 25.3 + - - +
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Residues in contact with LYS 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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271B ARG* 3.0 25.5 + - + +
272B LYS* 2.8 38.8 + - + +
274B ALA* 1.3 73.4 - - - +
276B LEU* 1.3 62.4 + - - +
278B HIS* 3.2 15.9 + - - +
279B GLU* 2.7 59.3 + - - +
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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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243B LEU* 3.9 9.0 - - + -
246B ARG* 4.1 34.8 - - + +
247B ILE* 4.1 27.8 - - + -
250B GLU* 4.2 20.0 - - + +
268B VAL* 4.9 2.2 - - + -
272B LYS* 2.6 48.9 + - + +
273B LYS* 3.7 7.6 - - - +
275B LYS* 1.3 73.5 - - - +
277B PHE* 1.3 63.2 + - - +
279B GLU* 3.3 19.9 + - - +
280B ILE* 3.1 25.8 + - + +
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Residues in contact with PHE 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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24B TYR* 4.8 5.2 - - + -
28B LEU* 3.5 32.5 - - + -
239B PRO* 4.0 25.8 - - + -
240B ILE* 4.5 9.0 - - + -
243B LEU* 3.7 30.6 - - + +
273B LYS 2.8 19.8 + - - +
274B ALA* 3.1 8.0 + - - +
276B LEU* 1.3 72.9 - - - +
278B HIS* 1.3 62.8 + - - +
280B ILE* 3.2 6.4 + - + +
281B ASN* 3.0 57.2 + - - -
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Residues in contact with HIS 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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274B ALA 2.9 13.2 + - - +
275B LYS* 3.4 21.0 + - - +
277B PHE* 1.3 78.0 - - - +
279B GLU* 1.3 67.8 + - - +
281B ASN* 3.3 6.8 + - - +
282B SER* 2.8 47.0 + - - -
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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
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246B ARG* 6.0 1.4 - - - -
272B LYS* 5.0 2.8 + - - -
275B LYS* 2.7 56.4 + - - +
276B LEU* 3.6 23.5 - - - +
278B HIS* 1.3 79.0 - - - +
280B ILE* 1.3 61.3 + - + +
282B SER* 3.3 13.5 + - - -
283B LYS* 3.3 22.0 - - - +
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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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239B PRO* 3.9 17.0 - - + +
242B GLU* 3.4 30.1 - - + +
243B LEU* 3.2 43.5 - - + +
246B ARG* 4.4 14.8 - - + +
276B LEU 3.1 17.4 + - - +
277B PHE* 3.2 9.1 + - + +
279B GLU* 1.3 76.8 - - + +
281B ASN* 1.3 61.5 + - - +
283B LYS* 3.0 30.5 - - - +
284B TYR* 3.1 36.3 - - + -
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Residues in contact with ASN 281 (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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239B PRO* 3.6 25.6 - - - +
277B PHE* 3.0 51.4 + - - +
278B HIS* 3.8 5.5 - - - +
279B GLU 3.3 0.2 - - - -
280B ILE* 1.3 73.3 - - - +
282B SER* 1.3 55.6 - - - +
283B LYS 2.7 10.5 + - - -
284B TYR* 3.3 30.4 + - + +
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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
----------------------------------------------------------
278B HIS* 2.8 42.6 + - - -
279B GLU* 3.6 9.6 - - - -
280B ILE 3.3 0.6 - - - -
281B ASN* 1.3 74.5 - - - +
283B LYS* 1.3 62.2 + - - +
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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