Contacts of the helix formed by residues 270 - 278 (chain X) in PDB entry 2W6C
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 LYS 270 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268X GLU 3.8 2.7 + - - +
269X LYS* 1.3 74.7 - - - +
271X PRO* 1.3 78.2 - - + +
272X GLN* 4.4 5.6 - - + +
273X GLU* 2.9 42.5 + - + +
274X LEU* 3.6 4.3 - - - +
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Residues in contact with PRO 271 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X ARG* 3.9 9.9 - - - +
68X GLN* 3.2 41.3 - - + +
92X GLU* 3.8 19.5 - - + +
153X PHE* 3.7 21.4 - - + -
269X LYS 3.5 0.6 - - - -
270X LYS* 1.3 87.8 - - + +
272X GLN* 1.3 62.3 + - - +
274X LEU* 3.0 18.0 + - + +
275X ILE* 3.2 11.2 + - - +
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Residues in contact with GLN 272 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X GLN* 4.9 2.8 + - - +
69X GLN 4.8 1.0 - - - +
90X MET* 4.5 14.4 - - - +
270X LYS* 3.2 5.5 + - + +
271X PRO* 1.3 79.5 - - - +
273X GLU* 1.3 59.3 + - + +
274X LEU 3.3 0.2 - - - -
275X ILE* 3.4 36.7 - - - +
276X ASP* 2.8 62.3 + - - +
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Residues in contact with GLU 273 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252X LEU* 3.7 24.7 - - + +
269X LYS* 3.9 24.6 + - + +
270X LYS* 2.9 44.9 + - + +
272X GLN* 1.3 78.5 - - + +
274X LEU* 1.3 69.9 + - + +
276X ASP* 3.4 13.5 + - - +
277X VAL* 3.7 8.1 + - - +
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Residues in contact with LEU 274 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X ARG* 4.2 6.3 - - - +
45X PHE* 3.9 30.3 - - + -
152X ALA* 4.8 8.4 - - + +
153X PHE* 4.3 20.6 - - + -
248X LEU* 4.5 18.6 - - + +
252X LEU* 4.2 15.3 - - + -
266X LEU* 4.2 11.0 - - + +
269X LYS* 3.3 38.6 - - + +
270X LYS 3.6 7.6 - - - +
271X PRO 3.0 6.8 + - - +
273X GLU* 1.3 77.6 - - + +
275X ILE* 1.3 64.0 + - - +
277X VAL* 3.4 5.7 + - - +
278X GLU* 3.2 22.8 + - - +
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Residues in contact with ILE 275 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X GLN* 4.1 10.5 - - + +
69X GLN* 3.7 36.1 - - - +
70X TYR* 3.8 38.7 - - + -
71X VAL 5.3 0.2 - - - +
153X PHE* 4.1 20.4 - - + -
271X PRO 3.2 15.2 + - - +
272X GLN* 3.4 34.1 - - - +
274X LEU* 1.3 79.5 - - - +
276X ASP* 1.3 63.3 + - - +
277X VAL 3.0 1.4 + - - -
278X GLU* 3.4 26.9 + - - +
279X TRP* 5.0 2.8 + - - -
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Residues in contact with ASP 276 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272X GLN* 2.8 49.8 + - - +
273X GLU* 3.9 8.4 - - - +
274X LEU 3.3 0.4 - - - -
275X ILE* 1.3 73.4 - - - +
277X VAL* 1.3 65.5 + - + +
280X ASN* 4.9 2.6 + - - +
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Residues in contact with VAL 277 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248X LEU* 3.7 19.3 - - + -
251X ASN* 3.7 30.5 - - + +
252X LEU* 3.9 17.9 - - + -
273X GLU 3.7 15.2 + - - +
274X LEU 4.0 1.1 - - - +
275X ILE 3.1 0.6 - - - -
276X ASP* 1.3 84.8 - - + +
278X GLU* 1.3 65.5 + - - +
279X TRP 3.2 2.9 - - - -
280X ASN* 2.9 41.2 + - - +
281X VAL* 4.5 4.7 + - - +
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Residues in contact with GLU 278 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X GLN* 5.9 0.2 - - - -
70X TYR* 4.4 11.4 + - - +
121X TYR* 3.2 34.3 - - - +
151X GLY* 4.1 17.1 - - - -
152X ALA* 5.0 2.3 + - + -
248X LEU* 4.6 4.9 - - - -
274X LEU 3.2 15.1 + - - +
275X ILE* 3.4 26.0 + - - +
277X VAL* 1.3 76.1 - - - +
279X TRP* 1.3 71.7 + - + +
281X VAL* 3.2 14.2 - - - +
291X SER* 2.6 32.3 + - - +
292X PHE* 3.9 23.6 + - + -
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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