Contacts of the helix formed by residues 303 - 309 (chain A) in PDB entry 6DWM
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 SER 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A GLN* 4.0 4.0 + - - -
292A LYS* 4.3 1.6 - - - +
301A GLN 3.6 5.5 + - - -
302A LEU* 1.3 78.5 - - - +
304A ASP* 1.3 67.3 + - - +
305A GLU* 3.3 9.8 + - - +
306A LYS* 3.2 35.4 + - - +
307A ILE* 3.4 19.1 + - - +
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Residues in contact with ASP 304 (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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289A CYS* 3.9 30.2 - - - +
292A LYS* 4.5 11.4 + - - +
303A SER* 1.3 74.7 - - - +
305A GLU* 1.3 63.0 + - - +
307A ILE* 3.4 1.5 + - - +
308A ILE* 3.2 30.1 + - - +
603A CPS 3.8 42.3 + - + +
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Residues in contact with GLU 305 (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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117A ASN* 3.1 23.0 + - - +
119A GLN* 3.0 28.3 + - - +
259A TYR* 2.8 27.5 + - - +
262A MET* 6.0 0.4 - - + -
303A SER* 3.1 9.2 + - - +
304A ASP* 1.3 79.8 - - - +
306A LYS* 1.3 56.4 + - - +
308A ILE* 3.2 4.5 + - - +
309A ASN* 3.0 36.6 + - + +
603A CPS 3.5 40.8 - - + +
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Residues in contact with LYS 306 (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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119A GLN* 3.4 31.9 - - + +
126A ASP* 5.2 4.4 + - - +
130A VAL* 4.6 19.7 - - + +
134A ARG* 3.1 47.3 + - - +
301A GLN 5.1 6.1 + - - +
302A LEU* 5.0 4.3 - - + -
303A SER* 3.2 30.8 + - - +
305A GLU* 1.3 75.7 - - - +
307A ILE* 1.3 58.5 + - - +
309A ASN* 3.2 15.2 - - - +
310A ILE* 3.3 7.4 - - - +
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Residues in contact with ILE 307 (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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137A LEU* 4.3 4.7 - - + -
285A LEU* 3.3 54.3 - - + +
288A HIS* 3.6 30.3 - - + +
289A CYS* 4.1 13.7 - - - -
292A LYS* 4.2 12.1 - - + +
302A LEU* 3.5 46.7 - - + +
303A SER 3.4 8.1 + - - +
304A ASP* 3.4 6.5 + - - +
305A GLU 3.2 0.6 - - - -
306A LYS* 1.3 77.0 - - - +
308A ILE* 1.3 63.4 + - - +
310A ILE* 3.6 11.6 - - + +
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Residues in contact with ILE 308 (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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262A MET* 4.1 9.6 - - + -
266A VAL* 3.5 30.1 - - + -
282A THR* 5.0 1.3 - - + +
285A LEU* 3.8 9.2 - - + +
286A ILE* 4.0 24.0 - - + +
289A CYS* 3.8 22.2 - - - -
304A ASP 3.2 18.4 + - - +
305A GLU 3.2 2.0 + - - +
307A ILE* 1.3 75.8 - - - +
309A ASN* 1.3 59.9 + - - +
310A ILE 2.9 10.9 + - - -
311A VAL* 3.2 26.1 + - + +
603A CPS 3.8 42.6 - - + -
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Residues in contact with ASN 309 (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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116A SER* 4.1 8.7 + - - +
119A GLN* 2.9 35.3 + - - +
120A SER* 5.3 0.4 - - - -
121A MET 5.0 0.7 + - - -
134A ARG* 3.0 20.3 + - - +
259A TYR* 3.6 29.6 + - + +
262A MET* 3.6 20.0 - - - -
305A GLU* 3.0 21.2 + - - +
306A LYS* 3.2 6.2 - - - +
308A ILE* 1.3 74.0 - - - +
310A ILE* 1.3 68.2 + - - +
311A VAL 3.2 0.7 - - - -
312A LEU* 3.1 17.1 + - + +
313A ASP* 3.5 9.5 + - - +
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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