Contacts of the helix formed by residues 285 - 293 (chain C) in PDB entry 4H0N
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 THR 285 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C GLU* 2.5 29.2 + - - +
202C VAL* 3.8 20.0 - - + -
206C PHE* 3.5 32.3 - - + -
282C ARG* 4.2 0.9 - - - +
284C PHE* 1.3 76.6 - - - +
286C PRO* 1.3 75.8 - - - +
287C LYS* 3.3 3.2 + - - -
288C GLU* 3.0 25.1 + - - +
289C VAL* 3.0 21.8 + - - +
311C TYR* 3.4 2.5 - - - -
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Residues in contact with PRO 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C PHE* 3.6 16.4 - - + -
285C THR* 1.3 89.1 - - - +
287C LYS* 1.3 61.1 + - - +
289C VAL* 4.4 0.9 - - + -
290C LEU* 3.0 31.1 + - - +
301C LEU* 3.7 24.9 - - + -
307C MET* 5.3 3.4 - - + -
310C CYS* 4.1 21.3 - - + -
311C TYR* 3.5 20.0 - - + +
314C LEU* 3.7 16.0 - - + +
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Residues in contact with LYS 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ILE 6.0 1.6 - - - +
199C GLU* 3.2 37.5 - - + +
285C THR* 3.3 1.3 + - - +
286C PRO* 1.3 80.6 - - - +
288C GLU* 1.3 60.3 + - + +
290C LEU* 3.8 9.5 + - + +
291C MET* 3.3 33.3 + - + +
300C ASN* 6.3 1.0 - - - +
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Residues in contact with GLU 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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197C ILE* 3.5 19.8 - - + +
198C ILE* 3.2 8.1 - - - +
199C GLU* 3.0 41.0 + - + +
282C ARG* 2.9 38.8 + - - -
284C PHE* 3.3 20.7 - - + +
285C THR* 3.0 27.9 + - - +
287C LYS* 1.3 77.8 - - + +
289C VAL* 1.3 59.8 + - - +
291C MET* 3.2 4.8 + - - +
292C ILE* 2.8 32.5 + - - +
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Residues in contact with VAL 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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232C PHE* 4.0 37.0 - - + -
284C PHE* 3.9 20.4 - - + +
285C THR 3.0 22.2 + - - +
288C GLU* 1.3 72.1 - - - +
290C LEU* 1.3 60.8 + - - +
292C ILE* 3.1 9.6 + - - +
293C MET* 2.8 44.8 + - + +
311C TYR* 4.4 12.1 - - + -
314C LEU* 3.7 26.9 - - + -
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Residues in contact with LEU 290 (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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12C ILE* 4.7 1.6 - - + -
286C PRO 3.0 22.4 + - - +
287C LYS* 3.8 9.2 - - + +
289C VAL* 1.3 77.1 - - - +
291C MET* 1.3 57.6 + - + +
293C MET* 3.2 4.1 + - - -
294C CYS 2.9 22.2 + - - -
295C PHE* 3.0 55.7 + - + -
299C TYR* 3.9 27.8 - - + +
300C ASN* 4.8 0.9 - - - -
301C LEU* 3.8 29.6 - - + +
314C LEU* 3.5 22.7 - - + -
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Residues in contact with MET 291 (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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154C VAL* 5.6 0.3 - - - +
196C SER 5.7 2.9 - - - +
197C ILE* 3.7 36.0 - - + +
287C LYS* 3.3 22.4 + - + +
288C GLU* 3.2 8.8 + - - +
290C LEU* 1.3 74.7 - - - +
292C ILE* 1.3 66.9 + - - +
294C CYS* 3.1 16.2 + - - +
295C PHE 4.1 15.5 - - - +
296C PRO 5.1 0.4 - - - +
297C LYS* 3.8 39.5 - - + +
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Residues in contact with ILE 292 (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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154C VAL* 3.3 27.4 - - + +
155C PRO* 4.7 2.5 - - + +
156C ASN* 3.7 34.3 - - + +
194C LEU* 4.1 16.4 - - + -
197C ILE* 3.6 25.6 - - + -
229C SER* 4.7 3.1 - - - +
232C PHE* 3.9 28.5 - - + -
284C PHE* 4.0 26.2 - - + -
288C GLU 2.8 23.5 + - - +
289C VAL* 3.1 8.3 + - - +
291C MET* 1.3 72.8 - - - +
293C MET* 1.3 61.5 + - + +
294C CYS* 3.5 0.9 + - - -
319C ASN* 3.7 2.6 + - - -
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Residues in contact with MET 293 (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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156C ASN* 5.2 4.5 - - - +
158C ARG* 4.2 25.8 - - - +
232C PHE* 5.5 3.6 - - + -
289C VAL* 2.8 29.8 + - + +
290C LEU 3.2 2.4 + - - +
292C ILE* 1.3 80.6 - - + +
294C CYS* 1.3 68.8 + - - +
295C PHE* 3.3 25.8 + - + -
314C LEU* 3.6 52.5 - - + +
317C SER* 4.5 3.6 - - - -
318C VAL 4.0 12.6 - - - +
319C ASN* 3.6 12.9 - - - +
320C VAL 3.1 21.7 + - - -
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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