Contacts of the helix formed by residues 199 - 206 (chain B) in PDB entry 5FQD
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 LEU 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A ILE* 6.4 0.2 - - + -
312A GLU* 3.8 11.2 - - - +
327A ARG* 3.4 52.9 - - + +
328A LEU* 4.2 29.4 - - + -
198B GLN* 1.4 78.4 - - - +
200B GLU* 1.3 60.9 + - - +
201B SER* 3.2 1.1 - - - +
202B LEU* 3.0 49.3 + - + +
203B ASN 3.5 6.8 + - - -
233B HIS* 5.7 2.7 - - + +
234B CYS* 3.4 9.5 - - - -
236B ASN* 5.9 1.1 - - - +
237B LEU* 3.9 20.4 - - + -
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Residues in contact with GLU 200 (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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16A ASN* 3.5 23.9 - - + +
62A ALA* 5.3 11.0 - - - +
312A GLU* 3.1 17.1 + - - +
327A ARG* 3.1 28.7 + - - -
198B GLN 3.5 11.1 - - - +
199B LEU* 1.3 70.3 - - - +
201B SER* 1.4 57.9 + - - +
203B ASN* 3.3 38.9 + - - +
204B LYS* 4.5 3.6 + - - -
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Residues in contact with SER 201 (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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259A VAL* 3.5 32.0 - - - +
311A ALA 4.6 0.9 + - - -
312A GLU* 2.8 48.4 + - - -
199B LEU* 4.3 2.1 - - - +
200B GLU* 1.4 74.4 - - - +
202B LEU* 1.4 72.7 + - - +
203B ASN 3.4 1.1 + - - -
204B LYS* 2.8 32.6 + - - +
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Residues in contact with LEU 202 (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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259A VAL* 3.8 14.4 - - + -
276A MET* 3.8 34.8 - - + -
198B GLN* 3.5 12.6 - - - +
199B LEU* 3.0 20.9 + - + +
201B SER* 1.4 87.2 - - - +
203B ASN* 1.3 62.1 + - - +
204B LYS 3.3 2.5 - - - -
205B CYS* 3.3 17.3 + - + +
206B GLN* 3.1 21.9 + - - +
233B HIS* 3.3 35.0 - - + +
234B CYS* 3.8 18.6 - - - -
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Residues in contact with ASN 203 (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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117A GLU 4.6 3.6 - - - +
118A THR* 2.9 51.9 + - + +
119A GLY* 4.0 11.1 + - - -
120A ILE 4.6 8.1 + - - +
198B GLN* 3.5 23.9 - - - +
199B LEU 3.5 1.1 + - - +
200B GLU* 3.3 37.8 + - - +
201B SER 3.4 1.4 - - - -
202B LEU* 1.3 77.3 - - - +
204B LYS* 1.4 56.5 + - - +
205B CYS 3.1 4.2 + - - -
206B GLN* 3.2 17.5 + - - +
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Residues in contact with LYS 204 (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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118A THR* 3.7 10.7 - - + +
165A ILE* 3.3 30.8 - - - +
166A ASP* 4.0 14.6 - - + +
188A ARG* 4.7 4.0 + - - -
217A SER* 3.3 45.5 - - - +
218A MET* 3.6 24.2 - - + -
258A ILE 4.9 1.1 - - - -
259A VAL* 3.1 24.5 + - - +
260A CYS* 5.2 0.4 - - - +
200B GLU 4.5 2.8 + - - -
201B SER* 2.8 35.5 + - - +
203B ASN* 1.4 76.0 - - - +
205B CYS* 1.4 61.9 + - - +
206B GLN 3.5 0.4 - - - -
207B ILE 4.8 3.1 + - - +
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Residues in contact with CYS 205 (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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217A SER* 4.9 5.4 - - - -
257A THR* 4.1 17.0 - - - -
259A VAL* 4.2 9.9 - - - -
276A MET* 4.0 27.6 - - + -
202B LEU* 3.5 18.4 - - + +
203B ASN 3.1 0.8 - - - -
204B LYS* 1.4 84.4 - - - +
206B GLN* 1.3 66.9 + - - +
207B ILE 3.3 3.5 + - - -
208B PHE* 3.6 6.8 - - - -
230B ARG* 3.0 43.0 + - + +
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Residues in contact with GLN 206 (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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117A GLU* 3.6 30.4 - - + +
118A THR* 4.7 0.4 - - - +
198B GLN* 3.4 34.5 + - + +
202B LEU* 3.1 22.0 + - - +
203B ASN* 3.2 21.6 + - - +
205B CYS* 1.3 82.1 + - - +
207B ILE* 1.3 59.3 + - - +
208B PHE* 3.3 23.9 + - - -
230B ARG* 3.6 18.7 + - - +
231B LYS* 3.8 19.9 - - - +
233B HIS* 5.9 0.8 - - - +
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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