Contacts of the helix formed by residues 259 - 267 (chain R) in PDB entry 5FYW
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 VAL 259 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B THR* 5.7 2.2 - - + -
99B LYS* 4.9 15.9 - - + +
100B PRO 5.6 0.2 - - - +
101B MET* 3.5 46.4 - - + -
109B THR* 4.2 8.0 - - + +
110B HIS* 5.2 3.8 - - - -
111B ALA* 5.4 8.3 - - + +
180B TYR* 4.9 11.7 - - - +
255R LEU 5.4 2.9 - - - +
257R GLU* 2.9 23.5 - - - +
258R THR* 1.3 78.5 + - - +
260R GLY* 1.3 61.2 + - - +
261R VAL 3.4 0.8 - - - +
262R THR* 2.7 30.5 + - - +
263R MET* 3.2 9.7 + - - +
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Residues in contact with GLY 260 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B THR* 4.5 18.3 + - - -
244M SER* 3.1 27.4 - - - +
245M HIS* 4.0 0.2 - - - -
247M GLY* 4.6 3.6 - - - -
258R THR* 2.8 13.4 + - - -
259R VAL* 1.3 76.7 - - - +
261R VAL* 1.3 59.6 + - - +
263R MET* 3.3 2.9 + - - +
264R SER* 2.9 27.0 + - - -
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Residues in contact with VAL 261 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M HIS 3.2 22.4 - - - +
246M LEU* 4.3 11.7 - - + +
301M THR* 5.6 3.8 - - + -
257R GLU* 5.5 8.1 - - + -
258R THR* 4.1 13.6 + - - +
259R VAL 3.4 0.2 - - - -
260R GLY* 1.3 75.1 - - - +
262R THR* 1.3 67.2 + - + +
264R SER* 2.4 20.5 + - - +
265R HIS* 3.0 29.5 + - + +
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Residues in contact with THR 262 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B THR* 5.1 3.1 - - + +
101B MET* 4.8 2.9 - - - +
129B PHE* 3.9 22.2 - - + -
255R LEU* 4.4 24.0 - - + -
257R GLU* 4.6 19.3 - - + +
259R VAL* 2.7 36.9 + - - +
261R VAL* 1.3 76.7 - - + +
263R MET* 1.3 64.2 + - - +
265R HIS* 3.2 10.7 + - - +
266R THR* 3.0 25.0 + - - +
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Residues in contact with MET 263 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B MET* 3.3 38.8 - - + -
103B ASN* 5.9 1.1 - - - -
109B THR* 3.5 30.1 - - + +
129B PHE* 5.5 0.7 - - + -
166B PHE* 3.5 32.1 - - + -
169B ARG* 3.5 25.1 - - - +
141M GLU* 4.7 8.7 - - - +
259R VAL 3.2 8.3 + - - +
260R GLY 3.9 2.5 - - - +
262R THR* 1.3 78.9 + - - +
264R SER* 1.3 67.2 + - - +
266R THR* 2.2 42.9 + - + -
267R GLY* 3.1 5.7 + - - -
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Residues in contact with SER 264 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M HIS* 3.1 55.4 + - - +
301M THR* 5.1 3.7 - - - +
260R GLY 2.9 6.2 + - - -
261R VAL* 2.4 27.8 + - - +
263R MET* 1.3 76.7 - - - +
265R HIS* 1.3 69.5 + - - +
267R GLY* 3.7 7.3 + - - +
268R MET 4.2 1.9 - - - +
269R SER* 3.4 23.0 + - - -
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Residues in contact with HIS 265 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PHE* 6.1 1.3 - - + -
164B LYS 5.8 3.4 - - - +
445B LYS* 4.6 4.9 - - - -
301M THR* 4.8 13.9 + - + +
261R VAL* 3.0 37.7 + - + +
262R THR* 3.2 8.3 + - - +
264R SER* 1.3 87.3 + - - +
266R THR* 1.3 63.2 + - + +
267R GLY 3.4 5.5 - - - +
269R SER* 4.1 15.3 + - - -
271R ARG* 3.5 34.1 + - - -
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Residues in contact with THR 266 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PHE* 3.4 32.1 - - + -
166B PHE* 3.6 25.9 - - + +
445B LYS* 4.2 12.8 - - - +
141M GLU* 4.6 5.4 + - - -
262R THR 3.0 16.1 + - - +
263R MET* 2.2 52.1 + - - -
265R HIS* 1.3 79.7 - - - +
267R GLY* 1.3 65.6 + - - +
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Residues in contact with GLY 267 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B LYS* 3.1 13.8 + - - -
139M ALA 5.3 8.7 - - - -
140M ALA 5.5 4.0 - - - -
141M GLU* 4.9 10.3 - - - -
263R MET 3.1 6.3 + - - -
264R SER 3.7 1.6 - - - +
265R HIS 3.4 4.7 - - - +
266R THR* 1.3 90.3 + - - +
268R MET* 1.3 68.0 + - - -
269R SER 3.0 4.2 + - - -
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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