Contacts of the helix formed by residues 280 - 289 (chain C) in PDB entry 6DWN
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 280 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C PHE* 3.4 24.2 - - - -
200C ALA 4.3 4.0 - - - +
201C ILE 3.8 7.9 - - - +
202C CYS 2.7 25.0 - - - +
203C PHE* 3.0 19.6 - - - -
204C GLY* 4.1 9.6 - - - +
269C HIS* 3.0 16.6 + - - -
279C ARG* 1.3 83.5 - - - +
281C ILE* 1.3 65.0 + - - +
282C THR* 3.5 3.8 - - - -
283C ASP* 3.2 26.2 + - - +
284C SER 3.2 16.5 + - - -
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Residues in contact with ILE 281 (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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137C LEU 5.8 0.9 - - - +
138C ALA* 6.2 1.1 - - - -
141C GLY* 3.6 29.6 - - - +
142C LEU* 3.7 22.4 - - + -
145C PHE* 4.1 4.3 - - + -
201C ILE* 3.3 38.5 + - + +
202C CYS* 3.8 7.2 + - - +
280C ASP* 1.3 75.3 - - - +
282C THR* 1.3 65.3 + - - +
284C SER* 2.9 25.4 + - - +
285C LEU* 3.1 20.8 + - + +
310C ILE* 5.8 1.1 - - + -
311C VAL* 3.7 21.5 - - + -
314C LEU* 4.1 15.9 - - + -
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Residues in contact with THR 282 (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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202C CYS 2.8 20.2 + - - -
203C PHE* 3.3 20.4 - - + -
265C MET 5.0 1.1 - - - +
266C VAL* 4.5 19.7 - - + -
269C HIS* 3.6 24.9 - - + +
280C ASP* 3.2 12.0 - - - -
281C ILE* 1.3 79.0 - - - +
283C ASP* 1.3 56.0 + - - +
285C LEU* 3.4 5.5 + - - +
286C ILE* 2.9 40.3 + - + +
308C ILE* 4.9 3.1 - - + +
311C VAL* 3.9 12.4 - - + +
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Residues in contact with ASP 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C HIS* 3.4 20.1 - - - +
273C PHE* 4.1 17.6 - - + -
277C HIS 4.0 3.6 - - - +
278C ILE* 3.6 16.6 - - + -
279C ARG* 2.7 48.4 + - - +
280C ASP* 3.2 21.5 + - - +
281C ILE 3.2 0.4 - - - -
282C THR* 1.3 74.0 - - - +
284C SER* 1.3 54.6 + - - +
285C LEU 3.1 1.8 - - - -
286C ILE* 3.1 6.7 + - - +
287C GLU* 2.6 38.0 + - - +
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Residues in contact with SER 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 5.6 1.6 + - - +
141C GLY* 4.3 12.9 - - - -
145C PHE* 4.2 9.6 - - - -
278C ILE* 3.4 15.6 - - - +
280C ASP 3.2 11.0 + - - -
281C ILE* 2.9 26.3 + - - +
283C ASP* 1.3 75.6 - - - +
285C LEU* 1.3 61.3 + - - +
287C GLU* 3.8 11.8 - - - +
288C HIS* 3.4 21.1 + - - +
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Residues in contact with LEU 285 (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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137C LEU* 4.4 23.3 - - + +
281C ILE* 3.1 24.1 + - + +
282C THR* 3.8 4.5 - - - +
283C ASP 3.1 0.4 - - - -
284C SER* 1.3 81.3 - - - +
286C ILE* 1.3 64.2 + - - +
287C GLU 3.2 0.9 - - - -
288C HIS* 3.2 13.1 + - + +
289C CYS* 3.2 17.8 + - - -
307C ILE* 3.3 40.9 - - + +
308C ILE* 4.1 15.0 - - + +
310C ILE* 4.0 26.2 - - + -
311C VAL* 3.9 24.0 - - + -
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Residues in contact with ILE 286 (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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266C VAL* 4.2 13.5 - - + +
269C HIS* 4.0 18.2 - - + -
270C TYR* 4.0 36.1 - - + +
273C PHE* 4.0 23.1 - - + -
282C THR* 2.9 37.7 + - + +
283C ASP* 3.6 7.6 - - - +
285C LEU* 1.3 73.7 - - - +
287C GLU* 1.3 63.5 + - - +
289C CYS* 3.0 28.3 + - + +
308C ILE* 3.9 16.6 - - + -
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Residues in contact with GLU 287 (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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273C PHE* 4.3 13.2 - - + -
275C LYS* 4.2 9.1 - - + +
278C ILE* 3.3 38.5 - - + +
283C ASP 2.6 20.9 + - - +
284C SER* 3.8 14.0 - - - +
286C ILE* 1.3 75.4 - - - +
288C HIS* 1.3 61.1 + - - +
289C CYS 3.5 5.5 + - - +
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Residues in contact with HIS 288 (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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137C LEU* 3.8 33.8 - - + +
284C SER 3.4 12.5 + - - +
285C LEU* 3.2 11.3 + - - +
286C ILE 3.1 1.0 - - - -
287C GLU* 1.3 76.9 - - - +
289C CYS* 1.3 63.9 + - - +
307C ILE* 3.7 28.5 - - + +
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Residues in contact with CYS 289 (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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285C LEU 3.2 16.8 + - - -
286C ILE* 3.0 19.7 + - + +
287C GLU 3.8 4.7 - - - +
288C HIS* 1.3 81.4 - - - +
304C ASP* 3.2 51.8 - - - +
307C ILE* 4.4 14.6 - - - -
308C ILE* 4.4 11.2 - - - -
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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