Contacts of the helix formed by residues 264 - 276 (chain C) in PDB entry 4H9Q
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 TYR 264 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262C THR* 3.0 17.8 + - - +
263C ARG* 1.3 99.3 - - + +
265C PRO* 1.3 68.4 - - + +
266C GLU* 3.1 9.9 - - - +
267C VAL* 3.0 16.7 + - + -
268C ASN* 3.0 14.4 + - - -
302C LEU* 4.1 23.6 - - + -
304C LEU* 3.6 30.9 - - + +
308C GLN* 3.4 28.3 + - - -
312C MET* 4.0 17.3 - - + -
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Residues in contact with PRO 265 (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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263C ARG 3.6 10.3 - - - +
264C TYR* 1.3 84.9 - - + +
266C GLU* 1.3 67.8 + - - +
267C VAL 3.4 0.2 - - - -
268C ASN* 3.6 14.7 - - + +
269C ARG* 2.9 50.7 + - - +
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Residues in contact with GLU 266 (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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264C TYR* 3.8 11.6 - - - +
265C PRO* 1.3 90.2 - - - +
267C VAL* 1.3 66.4 + - - +
269C ARG* 3.4 27.3 + - - +
270C ARG* 3.1 22.2 + - - +
296C ALA* 4.1 6.1 - - + +
300C HIS* 3.6 43.0 - - + +
302C LEU* 4.0 24.3 - - + +
402C PO4 4.4 3.9 + - - -
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Residues in contact with VAL 267 (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 THR* 3.8 16.8 - - + +
264C TYR* 3.0 23.5 + - + +
266C GLU* 1.3 73.6 - - - +
268C ASN* 1.3 67.4 + - - +
270C ARG* 3.0 5.0 + - - +
271C ILE* 2.9 42.0 + - + +
293C VAL* 3.9 27.6 - - + +
296C ALA* 3.8 20.2 - - + -
297C ALA* 4.8 0.9 - - - +
302C LEU* 4.2 12.3 - - + -
304C LEU* 5.1 2.2 - - + -
312C MET* 4.2 13.0 - - - -
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Residues in contact with ASN 268 (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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259C TYR* 3.5 28.8 - - - +
260C ARG* 3.7 21.0 + - + +
262C THR* 2.7 60.7 + - - +
263C ARG 4.9 0.2 - - - -
264C TYR 3.0 12.9 + - - -
265C PRO* 3.6 17.6 - - + +
267C VAL* 1.3 75.5 - - - +
269C ARG* 1.3 56.6 + - - +
271C ILE* 3.3 1.9 + - - +
272C GLU* 2.9 31.3 + - - +
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Residues in contact with ARG 269 (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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256C ARG* 5.5 0.2 + - - -
265C PRO* 2.9 35.8 + - - +
266C GLU* 3.4 32.9 + - - +
267C VAL 3.2 0.2 - - - -
268C ASN* 1.3 74.8 - - - +
270C ARG* 1.3 59.2 + - - +
272C GLU* 3.3 7.6 + - - +
273C ARG* 2.9 55.8 + - - +
300C HIS* 4.7 1.6 + - - -
402C PO4 3.4 23.3 + - - -
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Residues in contact with ARG 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C GLU 3.1 9.6 + - - +
267C VAL 3.0 8.3 + - - +
269C ARG* 1.3 78.8 - - - +
271C ILE* 1.3 58.9 + - - +
273C ARG* 3.4 25.0 + - + +
274C LEU* 3.0 27.2 + - - +
292C ALA* 3.9 34.3 - - + +
295C LYS* 5.5 3.1 - - + -
296C ALA* 4.1 10.5 - - + +
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Residues in contact with ILE 271 (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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259C TYR* 3.6 42.4 - - + -
262C THR* 4.6 1.3 - - + -
267C VAL* 2.9 34.7 + - + +
268C ASN 3.7 5.8 - - - +
270C ARG* 1.3 75.7 - - - +
272C GLU* 1.3 59.4 + - - +
274C LEU* 3.1 12.0 + - + +
275C ILE* 3.0 31.5 + - + +
289C VAL* 4.6 11.4 - - + -
292C ALA* 4.6 7.9 - - + -
293C VAL* 4.0 13.5 - - + +
316C ALA* 3.7 19.7 - - + -
320C VAL* 4.0 20.4 - - + -
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Residues in contact with GLU 272 (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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256C ARG* 3.0 30.9 + - - +
257C ILE 3.6 5.4 - - - +
258C PRO* 3.6 11.9 - - - +
259C TYR* 3.0 32.5 + - - +
260C ARG* 5.1 2.3 - - - +
268C ASN 2.9 16.9 + - - +
269C ARG* 3.7 6.9 - - - +
271C ILE* 1.3 77.0 - - - +
273C ARG* 1.3 61.6 + - - +
275C ILE* 3.5 8.9 - - - +
276C ASN* 2.7 45.1 + - - +
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Residues in contact with ARG 273 (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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256C ARG* 4.4 14.1 - - - +
269C ARG* 2.9 38.9 + - - +
270C ARG* 3.6 33.2 - - + +
272C GLU* 1.3 74.8 - - - +
274C LEU* 1.3 63.7 + - - +
276C ASN* 3.3 10.3 + - - -
277C LYS* 3.5 17.6 + - - +
402C PO4 2.9 48.8 + - - -
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Residues in contact with LEU 274 (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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270C ARG 3.0 14.7 + - - +
271C ILE* 3.1 13.0 + - + +
273C ARG* 1.3 78.2 - - - +
275C ILE* 1.3 62.2 + - + +
276C ASN 3.4 0.5 + - - -
277C LYS* 3.8 34.2 - - + +
282C THR* 3.8 12.3 - - - +
284C PRO* 3.8 29.0 - - + +
288C ASP* 3.8 36.3 - - + +
289C VAL* 3.9 14.8 - - + -
292C ALA* 4.3 10.8 - - + -
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 3.7 33.7 - - + +
259C TYR* 4.4 7.2 - - + -
271C ILE* 3.0 18.0 + - + +
272C GLU* 3.5 8.7 - - - +
274C LEU* 1.3 78.9 - - + +
276C ASN* 1.3 74.6 + - - +
277C LYS 3.6 0.9 - - - -
282C THR* 3.5 12.9 - - - +
284C PRO* 4.4 11.2 - - + -
320C VAL* 3.9 45.8 - - + -
324C LEU* 3.8 17.1 - - + +
327C ARG* 3.2 23.6 + - - -
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Residues in contact with ASN 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ARG* 3.3 34.9 + - + +
257C ILE* 2.7 47.4 + - - +
272C GLU* 2.7 33.7 + - - +
273C ARG* 3.3 3.6 + - - +
274C LEU 3.3 0.6 - - - -
275C ILE* 1.3 84.9 - - - +
277C LYS* 1.3 65.9 + - - +
278C PRO* 3.4 5.9 - - - +
327C ARG* 3.2 16.9 + - - +
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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