Contacts of the helix formed by residues 279 - 287 (chain A) in PDB entry 3F3Z
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 HIS 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A GLN* 3.2 31.4 - - + -
257A SER* 3.0 24.7 + - - -
258A LEU* 3.8 31.3 + - + +
261A ARG* 5.2 4.0 - - + +
271A ILE* 4.7 9.0 - - + -
275A GLN 3.6 3.6 + - - +
276A ALA* 3.0 21.1 + - - +
277A LEU 3.3 0.6 - - - +
278A GLU* 1.3 81.7 - - - +
280A GLU* 1.3 72.4 + - + +
281A TRP* 2.9 31.6 + - - +
282A PHE* 3.2 15.9 + - + +
283A GLU* 3.8 6.4 + - - +
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Residues in contact with GLU 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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254A GLN* 3.0 37.1 + - + +
278A GLU 3.6 1.6 + - - -
279A HIS* 1.3 80.6 + - + +
281A TRP* 1.3 66.4 + - - +
283A GLU* 3.1 12.7 + - + +
284A LYS* 2.9 40.3 + - + +
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Residues in contact with TRP 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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122A GLU* 3.0 40.6 + - - -
125A ALA* 3.7 13.9 - - + -
126A ALA* 3.4 21.1 - - + -
129A MET* 4.1 6.3 - - + -
214A MET* 3.5 38.1 - - + -
218A LEU* 4.3 10.3 - - + -
252A SER* 3.7 4.5 - - - -
254A GLN* 4.0 15.4 - - + +
255A ALA* 3.5 21.5 - - + +
258A LEU* 3.7 12.8 - - + -
279A HIS* 2.9 21.3 + - + +
280A GLU* 1.3 75.9 - - - +
282A PHE* 1.3 90.2 + + - +
284A LYS* 3.3 2.8 + - + +
285A GLN* 2.9 52.9 + - + +
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Residues in contact with PHE 282 (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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126A ALA* 3.3 28.3 - - + -
129A MET* 4.1 1.8 - - + -
130A LYS* 3.6 22.4 - - + -
133A LEU* 3.8 21.5 - - + -
258A LEU* 3.7 15.9 - - + -
276A ALA 3.2 31.9 - - - -
277A LEU* 3.8 19.1 - - + +
279A HIS* 3.2 12.2 + - + +
281A TRP* 1.3 100.5 - + - +
283A GLU* 1.3 57.9 + - - +
285A GLN* 4.8 2.5 - - - -
286A LEU* 2.9 49.0 + - + +
287A SER 3.9 0.2 + - - -
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Residues in contact with GLU 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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279A HIS 3.8 3.3 + - - +
280A GLU* 3.1 16.7 + - + +
282A PHE* 1.3 74.3 - - - +
284A LYS* 1.3 67.3 + - + +
287A SER* 3.0 36.1 + - - -
289A SER* 5.6 1.2 + - - -
291A ARG* 5.4 5.4 - - - +
292A ASN* 3.4 30.9 + - - +
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Residues in contact with LYS 284 (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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254A GLN* 3.9 20.0 - - + +
280A GLU* 2.9 46.7 + - + +
281A TRP* 3.7 6.1 - - - +
283A GLU* 1.3 78.1 - - + +
285A GLN* 1.3 70.6 + - - +
287A SER 4.9 1.4 + - - +
291A ARG 4.7 2.8 + - - -
292A ASN* 3.9 34.5 + - + +
294A LEU 2.8 34.6 + - - +
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Residues in contact with GLN 285 (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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122A GLU* 3.3 30.3 + - - +
123A SER* 3.2 42.3 + - - -
126A ALA* 3.5 21.5 - - + -
252A SER* 4.4 6.9 + - - -
281A TRP* 2.9 44.0 + - + +
282A PHE 4.3 0.2 - - - +
283A GLU 3.2 0.2 - - - -
284A LYS* 1.3 88.8 + - - +
286A LEU* 1.3 61.5 + - - +
287A SER 5.1 0.8 - - - +
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Residues in contact with LEU 286 (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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123A SER* 3.6 24.9 - - - +
126A ALA* 3.9 22.0 - - + +
127A ARG* 3.8 15.5 - - + +
130A LYS* 3.7 33.9 - - + +
282A PHE* 2.9 25.8 + - + +
285A GLN* 1.3 80.9 - - - +
287A SER* 1.3 65.7 + - - +
288A SER* 3.5 3.1 + - - -
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Residues in contact with SER 287 (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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282A PHE 3.9 1.2 + - - -
283A GLU* 3.0 31.2 + - - +
284A LYS 5.1 1.7 - - - +
285A GLN 5.1 1.0 - - - +
286A LEU* 1.3 78.6 + - - +
288A SER* 1.3 59.2 + - - +
289A SER* 3.1 21.9 + - - +
292A ASN* 2.9 30.5 + - - +
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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