Contacts of the helix formed by residues 276 - 284 (chain C) in PDB entry 5HP1
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 VAL 276 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261C VAL* 4.2 18.6 - - + +
264C LEU* 3.9 33.9 - - + -
265C ASN* 4.4 2.7 - - - +
274C ILE* 4.4 4.7 - - + -
275C LYS* 1.3 79.5 - - - +
277C ARG* 1.3 59.2 + - - +
279C LEU* 3.4 2.8 + - - -
280C SER* 2.5 47.0 + - - +
302C GLU* 3.2 7.6 - - - -
336C GLN* 3.8 1.2 + - - -
353C LYS* 3.4 18.8 - - - +
355C ALA* 5.6 1.8 - - + -
7E C 3.3 30.7 - - - +
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Residues in contact with ARG 277 (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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276C VAL* 1.3 78.3 - - - +
278C GLN* 1.3 75.1 + - - +
280C SER* 3.1 6.4 + - - -
281C LYS* 2.9 37.8 + - + +
284C ARG* 4.6 17.4 - - - +
302C GLU* 3.3 3.7 + - - +
334C GLN* 3.2 23.8 + - + +
335C GLY* 2.9 22.2 + - - -
336C GLN* 3.1 26.3 + - + +
355C ALA* 2.8 38.6 + - - +
357C MET* 4.7 13.5 - - - +
7E C 5.1 8.5 + - - -
8E T 4.7 13.7 + - - -
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Residues in contact with GLN 278 (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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277C ARG* 1.3 82.1 - - - +
279C LEU* 1.3 64.0 + - - +
281C LYS* 2.4 45.1 + - - +
282C LEU* 3.4 16.1 + - - +
296C THR* 4.9 2.7 + - - +
298C GLU* 3.5 34.8 - - + +
299C ALA* 3.6 23.2 - - + +
302C GLU* 2.9 24.0 + - + +
334C GLN* 3.3 26.7 + - - +
336C GLN* 5.3 0.2 - - - +
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Residues in contact with LEU 279 (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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257C ILE* 3.4 17.0 - - + +
260C LEU* 3.7 22.0 - - + -
261C VAL* 3.6 15.3 - - + -
264C LEU* 3.7 20.4 - - + -
275C LYS 4.0 3.4 - - - +
276C VAL* 3.8 4.3 - - - +
278C GLN* 1.3 72.1 - - - +
280C SER* 1.3 62.4 + - - +
282C LEU* 3.3 33.5 - - + +
283C LEU 3.5 0.9 + - - -
295C LEU* 5.7 3.4 - - + -
299C ALA 3.8 20.6 - - - +
302C GLU* 2.8 25.0 + - + +
303C LEU* 4.2 14.6 - - + +
306C ASN* 3.6 25.6 - - - +
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Residues in contact with SER 280 (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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261C VAL* 3.9 10.6 - - - +
276C VAL* 2.5 35.8 + - - +
277C ARG* 3.5 7.4 - - - -
279C LEU* 1.3 70.4 - - - +
281C LYS* 1.3 66.1 + - - +
283C LEU* 2.9 26.7 + - - +
284C ARG* 3.5 3.5 + - - +
7E C 3.1 42.9 - - - -
8E T 3.5 12.8 + - - +
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Residues in contact with LYS 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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277C ARG* 2.9 21.8 + - - +
278C GLN* 2.4 48.9 + - - +
280C SER* 1.3 78.0 - - - +
282C LEU* 1.3 64.3 + - + +
284C ARG* 2.9 55.5 + - - +
296C THR* 5.6 2.7 + - - -
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Residues in contact with LEU 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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257C ILE* 3.7 28.0 - - + -
278C GLN 3.5 7.9 - - - +
279C LEU* 3.3 22.2 - - + +
281C LYS* 1.3 77.5 - - + +
283C LEU* 1.3 62.4 + - - +
284C ARG 3.3 5.5 + - - +
293C ILE* 4.0 27.5 - - + +
294C PRO 4.1 9.9 - - - +
295C LEU* 3.9 15.0 - - + -
296C THR* 3.6 40.8 - - + +
299C ALA* 3.5 20.2 - - + -
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Residues in contact with LEU 283 (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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254C VAL* 3.7 27.8 - - + +
257C ILE* 3.6 26.2 - - + +
258C GLN* 3.5 45.5 - - + +
261C VAL* 4.7 10.8 - - + -
279C LEU 3.5 0.9 + - - +
280C SER* 2.9 23.5 + - - +
282C LEU* 1.3 78.1 - - - +
284C ARG* 1.3 63.5 + - - +
285C GLY 3.1 11.8 + - - +
293C ILE* 5.6 1.3 - - - -
7E C 5.9 3.4 - - - +
8E T 4.6 14.1 - - - +
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Residues in contact with ARG 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ARG* 4.6 14.5 - - - +
280C SER 3.6 7.6 - - - +
281C LYS* 2.9 48.9 + - - +
282C LEU 4.0 5.5 - - - +
283C LEU* 1.3 76.1 - - - +
285C GLY* 1.3 56.2 + - - +
357C MET* 6.3 0.8 - - - +
514C GLU* 5.7 5.1 + - - +
8E T 2.9 47.2 + - - +
9E T 3.3 20.5 + - - +
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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