Contacts of the helix formed by residues 304 - 309 (chain C) 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 ASP 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289C CYS* 3.4 38.0 - - - +
303C SER* 1.3 72.8 - - - +
305C GLU* 1.3 62.5 + - - +
307C ILE* 3.3 2.8 + - - +
308C ILE* 3.0 33.4 + - + +
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Residues in contact with GLU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ASN* 3.3 21.2 + - - +
119C GLN* 2.8 33.1 + - - +
259C TYR* 2.4 33.0 + - - +
262C MET* 6.1 1.1 - - + -
303C SER* 3.2 5.3 + - - +
304C ASP* 1.3 79.0 - - - +
306C LYS* 1.3 56.8 + - - +
308C ILE* 4.1 3.3 - - - +
309C ASN* 3.1 38.0 + - + +
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Residues in contact with LYS 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLN* 3.4 36.1 - - + +
126C ASP* 5.6 2.2 + - - +
130C VAL* 5.2 13.7 - - + +
134C ARG* 3.0 61.5 + - + +
303C SER* 3.2 28.7 + - - +
305C GLU* 1.3 74.6 - - - +
307C ILE* 1.3 59.0 + - + +
309C ASN* 3.3 7.0 - - - +
310C ILE* 3.4 7.6 - - - +
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Residues in contact with ILE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ARG* 5.7 3.8 - - + -
137C LEU* 4.1 15.7 - - + -
285C LEU* 3.4 53.6 - - + +
288C HIS* 3.9 25.6 - - + +
289C CYS* 4.1 15.5 - - - -
303C SER 3.1 28.8 + - - +
304C ASP* 3.8 4.7 - - - +
306C LYS* 1.3 81.6 - - + +
308C ILE* 1.3 62.0 + - - +
310C ILE* 3.6 10.5 - - - +
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C MET* 4.4 13.2 - - + -
266C VAL* 3.6 37.7 - - + -
282C THR* 5.0 1.8 - - + +
285C LEU* 4.0 10.2 - - + +
286C ILE* 4.1 30.7 - - + +
289C CYS* 4.0 20.9 - - - -
304C ASP* 3.0 23.1 + - + +
305C GLU* 3.3 4.2 + - - +
307C ILE* 1.3 74.7 - - - +
309C ASN* 1.3 58.8 + - - +
310C ILE 2.9 11.2 + - - -
311C VAL* 3.2 22.7 + - + +
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Residues in contact with ASN 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C SER* 4.1 14.8 + - - +
119C GLN* 3.0 33.6 + - - +
120C SER* 5.3 0.7 - - - -
121C MET 4.9 1.0 + - - -
134C ARG* 3.2 19.4 + - - +
259C TYR* 4.3 15.1 + - + +
262C MET* 3.6 25.1 - - + +
305C GLU* 3.1 18.4 + - - +
306C LYS* 3.3 7.1 - - - +
308C ILE* 1.3 74.4 - - - +
310C ILE* 1.3 69.3 + - - +
311C VAL 3.2 1.1 - - - -
312C LEU* 3.1 13.5 + - + +
313C ASP* 3.3 15.4 + - - +
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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