Contacts of the helix formed by residues 297 - 306 (chain C) in PDB entry 4D2W
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 ASN 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291C SER* 4.1 3.4 - - - -
296C ASN* 1.4 74.9 - - - +
298C ARG* 1.4 62.5 + - - +
299C GLN* 3.3 37.2 + - - +
300C THR* 2.7 25.3 + - - -
301C MET* 3.1 21.8 + - - +
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Residues in contact with ARG 298 (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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284C ASP* 3.1 45.3 + - - +
287C VAL* 3.5 18.9 - - - +
288C THR* 3.2 25.8 - - - +
291C SER* 4.3 9.2 + - - +
297C ASN* 1.4 71.5 - - - +
299C GLN* 1.4 62.5 + - - +
301C MET* 3.3 2.3 + - - +
302C GLU* 2.9 60.0 + - + +
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Residues in contact with GLN 299 (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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297C ASN* 3.3 14.3 + - - +
298C ARG* 1.4 77.5 - - - +
300C THR* 1.4 65.1 + - - +
302C GLU* 3.6 8.9 + - - +
303C ASP* 3.1 62.3 + - - +
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Residues in contact with THR 300 (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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296C ASN* 3.3 21.3 - - - +
297C ASN* 2.7 34.9 + - - +
299C GLN* 1.4 88.9 + - - +
301C MET* 1.3 60.0 + - - +
303C ASP* 3.8 4.1 - - - +
304C LEU* 3.2 31.7 + - + +
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Residues in contact with MET 301 (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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287C VAL* 3.8 15.9 - - + +
290C LEU* 3.8 20.6 - - + -
291C SER* 3.4 22.7 - - - +
294C HIS* 3.7 34.5 - - + +
296C ASN* 3.1 18.3 - - - +
297C ASN 3.1 7.8 + - - +
298C ARG 3.8 2.9 - - - +
300C THR* 1.3 74.6 - - - +
302C GLU* 1.4 62.0 + - - +
304C LEU* 3.3 8.5 + - + +
305C ILE* 2.9 41.3 + - + +
313C LEU* 3.5 35.9 - - + -
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Residues in contact with GLU 302 (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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282C LEU* 3.8 28.5 - - + +
284C ASP* 4.5 8.1 - - - +
287C VAL* 3.8 16.6 - - + +
298C ARG* 2.9 54.3 + - - +
299C GLN* 4.0 7.0 - - - +
301C MET* 1.4 71.8 - - - +
303C ASP* 1.3 59.1 + - - +
305C ILE* 3.3 2.7 + - - -
306C SER* 2.9 35.4 + - - +
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Residues in contact with ASP 303 (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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299C GLN* 3.1 49.6 + - - +
300C THR* 3.8 4.7 - - - +
302C GLU* 1.3 76.7 - - - +
304C LEU* 1.3 62.2 + - + +
306C SER* 3.6 5.9 + - - -
307C LEU* 3.3 29.6 + - + +
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Residues in contact with LEU 304 (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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294C HIS* 4.8 9.6 - - + +
296C ASN* 4.4 15.5 - - - +
300C THR* 3.2 23.1 + - + +
301C MET* 3.5 17.0 - - + +
303C ASP* 1.3 74.2 - - + +
305C ILE* 1.4 65.6 + - - +
307C LEU* 3.4 32.1 + - + +
308C TRP 4.3 0.7 + - - -
309C GLN* 5.3 3.5 + - - +
313C LEU* 3.7 21.1 - - + +
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Residues in contact with ILE 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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282C LEU* 4.1 12.8 - - + -
287C VAL* 3.9 26.9 - - + -
290C LEU* 3.8 24.7 - - + -
301C MET* 2.9 30.6 + - + +
302C GLU* 3.3 3.6 + - - +
304C LEU* 1.4 74.1 - - - +
306C SER* 1.4 57.8 + - - +
308C TRP* 3.0 58.0 + - + -
313C LEU* 3.8 26.5 - - + -
314C THR* 5.1 1.3 + - - -
317C TYR* 3.9 15.9 - - + -
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Residues in contact with SER 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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279C PHE 5.3 1.5 + - - -
280C ILE 5.2 2.4 + - - -
282C LEU* 3.6 18.4 - - - +
302C GLU* 2.9 19.1 + - - +
303C ASP* 4.0 7.4 - - - -
304C LEU 3.3 0.4 - - - -
305C ILE* 1.4 71.3 - - - +
307C LEU* 1.4 64.8 + - - +
308C TRP* 3.2 23.3 - - - +
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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